I would say this is a toss up between Snowball and Boxer, but in the end I would have to come down on the side of Boxer. Boxer shows his courage as a fighter in the Battle of the Cowshed, frightening away Farmer Jones' men:
But the most terrifying spectacle of all was Boxer, rearing up on his hind legs and striking out with his great iron-shod hoofs like a stallion.
After the battle, he is awarded, as is Snowball, "Animal Hero, First Class."
Boxer also shows enormous courage as he faces the dauntingly hard work of building the windmill, becoming an inspiration to all the other animals:
To see him toiling up the slope inch by inch, his breath coming fast, the tips of his hoofs clawing at the ground, and his great sides matted with sweat, filled everyone with admiration. Clover warned him sometimes to be careful not to overstrain himself, but Boxer would never listen to her.
After the windmill falls down and has to be rebuilt, Boxer again shows courage: "Only Boxer and Clover never lost heart."
When Frederick's men attack, Boxer tries to rally the animals to fight. After the men blow up the second windmill, Boxer, along with many of the other animals, attacks them fearlessly.
Boxer is the only one who shows he is not afraid of the dogs who are about the rip up the rebellious hens, but tragically he decides to back down—not from fear but from feeling that Napoleon must always be right.
At various points, other animals match Boxer for courage, but he is the only one who always shows courage. He demonstrates his bravery in battle, a conventional way to show a courageous heart, but also in what sometimes takes more courage: facing the day-to-day struggles against all odds to achieve what seems an impossible task.