The Chocolate War
Brother Leon is the biggest villain in the book. Not only does he antagonize Jerry, but all the other students as well. Leon is much to blame for the general mood of domination and violence at Trinity. He's responsible for letting The Vigils get away with whatever they want. In fact, he encourages them and uses them to make students do what he wants them to do.
Archie Costello and The Vigils
Archie is an antagonist in his own right, but it's his affiliation with The Vigils that gives him the power to actively organize against Jerry.
Without Jerry, The Vigils, and Brother Leon, Jerry might never have appeared on Emile's radar. But, he does, and Emile (first with his friends, and then at the raffle) is the person who delivers the bulk of Jerry's physical punishment. These brutal beatings are a big part of what makes Jerry's story truly tragic.