Superman has the chest hair advantage and better taste in women. Clear winner.
On a slightly, but not really, more serious note, MoS Supes is a beast. His speed, mobility, and flight are unmatched on the big screen. The only ones that come close are his fellow Kryptonians and the Hulk, though other then Zod, no flight. He also seems pretty indestructible (I wonder if he could fly through a space whale the way he flew through the scout ship), but as we know both of these incarnations of Superman and Thor can be killed.
I wouldn't say Clark is necessarily stronger, but it is the combination of speed and strength that would give Thor a lot of trouble. Thor might be able to hit Clark as hard, but he'd have to catch him and probably would have to take a lot more shots for his one.
Thor's best weapon in this fight would be his lightning. It isn't as direct as Clark's heat vision, but so far it has more potential to do big damage. The one disadvantage when it comes to Thor's lightning in the films is that so far he must gather it using his hammer if he wants to direct it, and that takes a bit of time. Clark is just too fast for that.
Though I do wonder what would happen if Thor put up a spinning hammer guard. Could be tough for Clark to get around. Would have to get fancy with the heat vision.
In the end though, I think the answer is clear. Batman with prep time beats them both at the same time.