I'd say Al, because he was the one who set up the whole story from the get-go by stealing Woody in the first place; Stinky Pete, on the other hand, wasn't even revealed to also be a villain until the beginning of the climax.
But then again, can we really argue that either of them are really true villains? I mean, is Al a villain because he stole Woody to add to this collection, or is he a villain because he's a greedy opportunist who was trying to seal a quick-rich-quick deal? And Stinky Pete, is he a villain because of his grudge against the space age craze, or is he a villain because of his attempts to prevent Woody from escaping and going back home?
Interesting questions, are they not?