When most people think about Jesus, they have a mashup of scenes from all four gospels in their head. "The kingdom of God is at hand," healings, "I am the way, the truth, and the life," exorcisms, "Follow me," "You must be born again," the cleansing of the Temple, turning water into wine, "Give to Caesar what is Caesar's and give to God what is God's," "For God so loved the world..."
In historical Jesus studies, not all of the material in the gospels is given equal weight. And one gospel in particular – The Gospel of John – is cut out almost entirely as a source of historical information about Jesus. When historical Jesus scholars argue for their unique reconstruction, in regards to the canonical sources, they argue almost exclusively from Matthew, Mark, and Luke.
Before getting into the reasons why the synoptics (called so because they provide a "synopsis" of the life of Jesus from a unified perspective) are nearly universally seen as giving us our earliest, most accurate data, it will be helpful to look at how scholars believe they developed.
Although there is still some debate within the discipline, the graphic above is a pretty standard understanding of how the synoptic gospels developed. Mark is seen as our earliest gospel, often dated in the late 60s (dating is difficult however, and widely debated). "Q" (standing for "Quelle," which is German for "source") is a hypothetical (but widely believed to have existed) "sayings source" consisting of material that has identical wording in Matthew and Luke, but which is absent from Mark. Matthew is seen as using Mark, Q, and his own material to create his gospel, Luke using Mark, Q, and his own material to create his. You can explore the relationship between these gospels by using a synoptic parallel.
Occasionally the order of composition is challenged and dating debates never end, but this is the most common understanding of how Matthew, Mark, and Luke developed. Each of these gospels use much of the same material and follow the same basic chronology of events. The image of Jesus created in them is consistent.
John is a different beast.
Some of the primary differences in the Gospel of John include:
Style
Jesus speaks in long, soaring soliloquies in the Gospel of John. The parable-centric teacher of the synoptics disappears and is replaced by one who engages in extended dialogues with individuals and long, theologically heavy monologues. In a typical Bible, this can be seen by the large blocks of red text in comparison to the synoptics. The style of the Gospel of John almost has the feel of a play or production in comparison to the choppiness and unevenness of, for instance, the Gospel of Mark.
Specific Events and Chronology
While the synoptics contain mostly the same events, the Gospel of John contains many unique and memorable stories not found in other sources. For instance the stories of Jesus changing water into wine, the conversation with Nicodemus, the Samaritan woman at the well, Jesus saving the adulterous woman from being stoned, the raising of Lazarus, the healing of a man born blind, Jesus washing the disciples’ feet, and the resurrection appearance to Thomas are all unique to John. The chronology of John is also markedly different, most famously regarding the length of Jesus’ ministry (in the Gospel of John Jesus’ ministry lasts at least three years while in the synoptics it mostly takes place over the course of one year), and the timing of the cleansing of the Temple (in the Gospel of John Jesus cleanses the Temple at the beginning of his ministry, while in the synoptics this event takes place during the last week of his life).
The Message of Jesus
It is often claimed that, in the Gospel of John, “the proclaimer becomes the proclaimed.” That is, in the synoptic gospels, Jesus’ message is not primarily about himself, but, rather, about the kingdom of God. Both Matthew and Mark summarize Jesus’ message with the words “Repent, for the kingdom of God is at hand.” While the language of the kingdom of God doesn’t disappear completely from John, it is significantly muted and replaced by the message about Jesus. Jesus’ identity and the importance of believing in him are far more central to the theology of the Gospel of John than in the synoptics. It’s not that the message of Jesus is totally different, but the change in emphasis is very noticeable.
Christology
The Christology of the Gospel of John is consistently more advanced than in the synoptics. Personally, I would argue that the synoptics themselves have a high Christology (for instance, Jesus is depicted as the judge who will determine who enters the kingdom of God in Matthew 25), but only in the Gospel of John does Jesus become the Logos, co-equal with the Father. “I and the Father are one,” “the Word was God,” use of the Divine “I am,” etc. are language and concepts that are only found in the Gospel of John.
The Gospel of John is also widely viewed as the last gospel to have been written. It wouldn't make sense, for instance, for the synoptic authors to lower their Christology; we would expect the portrayal of Jesus, if anything, to become heightened over time (and we do see this in the synoptics in subtle ways, for instance compare Mark 6:5 – "he could not perform any miracles there," to the later Matthew 13:58 – "he did not do many miracles there," Matthew altering language which seems to limit Jesus' power). The author of the Gospel of John also seems to be aware of the death of both Peter and the disciple John (one reason that most don't believe John the disciple wrote all of the gospel, if any, despite the internal claim) which would lead to the belief that it was written quite late:
"Jesus said, “Feed my sheep. Very truly I tell you, when you were younger you dressed yourself and went where you wanted; but when you are old you will stretch out your hands, and someone else will dress you and lead you where you do not want to go.” Jesus said this to indicate the kind of death by which Peter would glorify God. Then he said to him, “Follow me!”
Peter turned and saw that the disciple whom Jesus loved was following them. (This was the one who had leaned back against Jesus at the supper and had said, “Lord, who is going to betray you?”) When Peter saw him, he asked, “Lord, what about him?”
Jesus answered, “If I want him to remain alive until I return, what is that to you? You must follow me.” Because of this, the rumor spread among the believers that this disciple would not die. But Jesus did not say that he would not die; he only said, “If I want him to remain alive until I return, what is that to you?”"
– John 21:17-23
It is unclear whether the writer or writers of the Gospel of John had access to the synoptic gospels. If he, or they, did have access, it doesn't seem like that material was used in any straightforward way.
Because of the significant differences between the synoptics and John, it seems that either the picture created by the synoptics gives us historically accurate information or John does. If Jesus said things like "I am the Way, the Truth, and the Life," or "I am the Vine and you are the branches," or "For God so loved the world that he gave his only begotten Son, the whoever believes in him shall not perish but have everlasting life," we would expect this kind of language to show up all over our sources. Scholars almost universally trust the synoptic gospels over the Gospel of John for historically accurate information about Jesus. You would really have to argue your case to try to convince those in the discipline that a specific incident from John is historically accurate. Even conservative scholars like N.T. Wright do not use the Gospel of John much, if at all, in their reconstructions of the historical Jesus. A recent publication from two well-known evangelical scholars/apologists (The Jesus Legend: A Case for the Historical Reliability of the Synoptic Jesus Tradition) makes the same point. It is only the synoptic tradition that is argued for.
Personally, I have come to see the Gospel of John as a type of abstract art about Jesus, perhaps faithfully continuing theological lines of trajectory from the synoptics, but not as a valuable source for finding historical information about Jesus.
But... just to throw a wrench in things, I will mention that there is one place in the synpotics where Jesus does sound strikingly like he does in John. The passage is sometimes called the Johannine Thunderbolt.
“All things have been committed to me by my Father. No one knows the Son except the Father, and no one knows the Father except the Son and those to whom the Son chooses to reveal him."
– Matt. 11:27, Luke 10:22
This saying, found identically in Matt. 11:27 and Luke 10:22, is thus also part of the hypothetical Q source! So there's your wrench.