Terminology:
The term Ίουδαῖος (Ioudaios) occurs 71 times in the Fourth Gospel, all but four of which are plural Ίουδαίοι (Ioudaioi):
 

The word Ίουδαία (Ioudaia, the geographical area of "Judea") also occurs six times: John 4:3, 47, 54; 7:1,3; 11:7

Referents:
However, in different passages, Ίουδαίοι (Ioudaioi) seems to refer to three different groups of people:

A)  specifically and only to the "Jewish leaders and authorities," rather than to the people as a whole;
B)  only or mainly to the people living in the geographical territory of Judea, that is, "the Judeans";
C)  to all members (or some or any in general) of the ethnic/religious group of people still called "Jews" today.

We should also recognize that not all of these verses are harshly negative, but some say very positive things about the Ioudaioi, while others could be classified as "neutral" statements.  Some say nice things about "the Jews" and/or the Jewish religion, some simply give factual information, while others do betray harsh/hostile attitudes.

Thus, reading each of these verses (and the surrounding passages), we should ask which of the above groups is most likely being referred to in each case, and whether the reference is positive, negative, or neutral.  To do this, one should consider whether the verse still says the same thing if in place of the word "Jews/Ioudaioi" we substitute the phrases:  A) "the Jewish leaders and authorities";  or B) "the Judeans" or "people living in the territory of Judea";  or C) "any or all religious and ethnic Jews."

Examples:
First example, John 1:19 - "This is the testimony given by John when the Jews sent priests and Levites from Jerusalem to ask him, 'Who are you?'" -  If we try substituting the underlined word here with the English translation, "all religious and ethnic Jews," the passage does not really make sense, since the average person or the people as a whole would not have had the authority to send priests and Levites on investigating missions; so option C) does not fit.  Similarly, even though Jerusalem is in Judea, it is not really "all people living in the territory of Judea" who send the priests and Levites, so choice B) is also out.  However, substituting with "the Jewish leaders and authorities" makes good sense in this verse, so 1:19 belongs in the list under category A).

Second example, when the phrase "King of the Jews" comes up, its political connotations suggest that it does not just mean "King of the Jewish authorities," nor "King of the religious Jews living anywhere," but rather, "King of the people of Judea"; so here the best option is category B).  Note that the six uses of the related term "Judea" (clearly referring to the geographical region), obviously belong in this category.

Third example, John 2:6 refers to the "Jewish rites of purification."  (Caution: here English uses an adjective "Jewish" to translate the original Greek phrase meaning "of the Jews," just like in 7:2, 18:12, and 19:42).  Does this really mean A) "purification rites of the Jewish leaders,"  or B) "purification rites of the people of Judea,"  or C) "purification rites of all religious/ ethnic Jews" in general?  Clearly, option C) makes the most sense.

“Anti-Semitism” in the Fourth Gospel?

Certain statements of John’s Gospel can be, and actually have been, misread in anti-Semitic ways. This happens especially when statements involving “the Jews” are taken to refer to ALL Jewish people, rather than just to some Jews, such as the chief priests and other first-century Jewish leaders.

• “The Jews” try to kill Jesus
• Jesus harshly criticizes “the Jews”

5:16-18 Therefore the Jews started persecuting Jesus, because he was doing such things on the sabbath. 17 But Jesus answered them, "My Father is still working, and I also am working." 18 For this reason the Jews were seeking all the more to kill him, because he was not only breaking the sabbath, but was also calling God his own Father, thereby making himself equal to God.

5:36-47 But I have a testimony greater than John's. The works that the Father has given me to complete, the very works that I am doing, testify on my behalf that the Father has sent me. 37 And the Father who sent me has himself testified on my behalf. You have never heard his voice or seen his form, 38 and you do not have his word abiding in you, because you do not believe him whom he has sent. 39 "You search the scriptures because you think that in them you have eternal life; and it is they that testify on my behalf. 40 Yet you refuse to come to me to have life. 41 I do not accept glory from human beings. 42 But I know that you do not have the love of God in you. 43 I have come in my Father's name, and you do not accept me; if another comes in his own name, you will accept him. 44 How can you believe when you accept glory from one another and do not seek the glory that comes from the one who alone is God? 45 Do not think that I will accuse you before the Father; your accuser is Moses, on whom you have set your hope. 46 If you believed Moses, you would believe me, for he wrote about me. 47 But if you do not believe what he wrote, how will you believe what I say?"

7:1 After this Jesus went about in Galilee. He did not wish to go about in Judea because the Jews were looking for an opportunity to kill him.

7:11-13 The Jews were looking for him at the festival and saying, "Where is he?" 12 And there was considerable complaining about him among the crowds. While some were saying, "He is a good man," others were saying, "No, he is deceiving the crowd." 13 Yet no one would speak openly about him for fear of the Jews.

7:19-20 "Did not Moses give you the law? Yet none of you keeps the law. Why are you looking for an opportunity to kill me?" 20 The crowd answered, "You have a demon! Who is trying to kill you?"

7:28 Then Jesus cried out as he was teaching in the temple, “You know me, and you know where I am from. I have not come on my own. But the one who sent me is true, and you do not know him.”

8:19-27 Then they said to him, "Where is your Father?" Jesus answered, "You know neither me nor my Father. If you knew me, you would know my Father also." 20 He spoke these words while he was teaching in the treasury of the temple, but no one arrested him, because his hour had not yet come. 21 Again he said to them, "I am going away, and you will search for me, but you will die in your sin. Where I am going, you cannot come." 22 Then the Jews said, "Is he going to kill himself? Is that what he means by saying, 'Where I am going, you cannot come'?" 23 He said to them, "You are from below, I am from above; you are of this world, I am not of this world. 24 I told you that you would die in your sins, for you will die in your sins unless you believe that I am he." 25 They said to him, "Who are you?" Jesus said to them, "Why do I speak to you at all? 26 I have much to say about you and much to condemn; but the one who sent me is true, and I declare to the world what I have heard from him." 27 They did not understand that he was speaking to them about the Father.

8:37-59 I know that you are descendants of Abraham; yet you look for an opportunity to kill me, because there is no place in you for my word. 38 I declare what I have seen in the Father's presence; as for you, you should do what you have heard from the Father." 39 They answered him, "Abraham is our father." Jesus said to them, "If you were Abraham's children, you would be doing what Abraham did, 40 but now you are trying to kill me, a man who has told you the truth that I heard from God. This is not what Abraham did. 41 You are indeed doing what your father does." They said to him, "We are not illegitimate children; we have one father, God himself." 42 Jesus said to them, "If God were your Father, you would love me, for I came from God and now I am here. I did not come on my own, but he sent me. 43 Why do you not understand what I say? It is because you cannot accept my word. 44 You are from your father the devil, and you choose to do your father's desires. He was a murderer from the beginning and does not stand in the truth, because there is no truth in him. When he lies, he speaks according to his own nature, for he is a liar and the father of lies. 45 But because I tell the truth, you do not believe me. 46 Which of you convicts me of sin? If I tell the truth, why do you not believe me? 47 Whoever is from God hears the words of God. The reason you do not hear them is that you are not from God." 48 The Jews answered him, "Are we not right in saying that you are a Samaritan and have a demon?" 49 Jesus answered, "I do not have a demon; but I honor my Father, and you dishonor me. 50 Yet I do not seek my own glory; there is one who seeks it and he is the judge. 51 Very truly, I tell you, whoever keeps my word will never see death." 52 The Jews said to him, "Now we know that you have a demon. Abraham died, and so did the prophets; yet you say, 'Whoever keeps my word will never taste death.' 53 Are you greater than our father Abraham, who died? The prophets also died. Who do you claim to be?" 54 Jesus answered, "If I glorify myself, my glory is nothing. It is my Father who glorifies me, he of whom you say, 'He is our God,' 55 though you do not know him. But I know him; if I would say that I do not know him, I would be a liar like you. But I do know him and I keep his word. 56 Your ancestor Abraham rejoiced that he would see my day; he saw it and was glad." 57 Then the Jews said to him, "You are not yet fifty years old, and have you seen Abraham?" 58 Jesus said to them, "Very truly, I tell you, before Abraham was, I am." 59 So they picked up stones to throw at him, but Jesus hid himself and went out of the temple.

10:1-13 "Very truly, I tell you, anyone who does not enter the sheepfold by the gate but climbs in by another way is a thief and a bandit. 2 The one who enters by the gate is the shepherd of the sheep. 3 The gatekeeper opens the gate for him, and the sheep hear his voice. He calls his own sheep by name and leads them out. 4 When he has brought out all his own, he goes ahead of them, and the sheep follow him because they know his voice. 5 They will not follow a stranger, but they will run from him because they do not know the voice of strangers." 6 Jesus used this figure of speech with them, but they did not understand what he was saying to them. 7 So again Jesus said to them, "Very truly, I tell you, I am the gate for the sheep. 8 All who came before me are thieves and bandits; but the sheep did not listen to them. 9 I am the gate. Whoever enters by me will be saved, and will come in and go out and find pasture. 10 The thief comes only to steal and kill and destroy. I came that they may have life, and have it abundantly. 11 "I am the good shepherd. The good shepherd lays down his life for the sheep. 12 The hired hand, who is not the shepherd and does not own the sheep, sees the wolf coming and leaves the sheep and runs away--and the wolf snatches them and scatters them. 13 The hired hand runs away because a hired hand does not care for the sheep.

10:19-21 Again the Jews were divided because of these words. 20 Many of them were saying, "He has a demon and is out of his mind. Why listen to him?" 21 Others were saying, "These are not the words of one who has a demon. Can a demon open the eyes of the blind?"

10:24 So the Jews gathered around him and said to him, "How long will you keep us in suspense? If you are the Messiah, tell us plainly." 25 Jesus answered, "I have told you, and you do not believe. The works that I do in my Father's name testify to me; 26 but you do not believe, because you do not belong to my sheep. 27 My sheep hear my voice. I know them, and they follow me. 28 I give them eternal life, and they will never perish. No one will snatch them out of my hand. 29 What my Father has given me is greater than all else, and no one can snatch it out of the Father's hand. 30 The Father and I are one." 31 The Jews took up stones again to stone him.

11:7 Then after this he said to the disciples, "Let us go to Judea again." 8 The disciples said to him, "Rabbi, the Jews were just now trying to stone you, and are you going there again?"

11:47 So the chief priests and the Pharisees called a meeting of the council, and said, "What are we to do? This man is performing many signs. 48 If we let him go on like this, everyone will believe in him, and the Romans will come and destroy both our holy place and our nation." 49 But one of them, Caiaphas, who was high priest that year, said to them, "You know nothing at all! 50 You do not understand that it is better for you to have one man die for the people than to have the whole nation destroyed." 51 He did not say this on his own, but being high priest that year he prophesied that Jesus was about to die for the nation, 52 and not for the nation only, but to gather into one the dispersed children of God. 53 So from that day on they planned to put him to death.

18:14 Caiaphas was the one who had advised the Jews that it was better to have one person die for the people.

(Cf. Matt 27:25 – “Then the people as a whole answered, ‘His blood be on us and on our children!’ ”)

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