I am studying the Gospel of John and am trying to connect its interpretation to the early church. What early church father has done the most and best commentary on the Gospel of John?
Ancient Literature section of the Passage Guide
This should start your research.
The obvious ones to me would be:
Origen: Incomplete, and questionably orthodox, yet brilliant.
John Chrysostom: Probably the most famous preacher in the early Greek church. His concerns and style are not what we are used to, but you can see more than a bit why when you read his sermons.
Cyril of Alexandria: A great theologian developing the Christology of the Church engages the Gospel with the richest Christology.
Augustine: The great figure who brought Classic learning to the West, and whose fingerprints are still on almost all of our Theology and Philosophy.
Please note that a few of the above are for the first volume of their work, and not all of their work on John. Look to see if there is a collection that includes the text I linked that makes sense to purchase, since if they are in a base package or library expansion, that might be the best way to get it. And at least some of these are also in the common ECF set in an older translations/editions. Pick what looks interesting to you.
If you have the Ancient Christian Commentary on John, it's excerpts should point you in the right direction. Similarly with Catena Aurea. You'll discover Ken gave you solid advice but there are a few others.