You'd also have to take into account where the battle takes place. It's canon that Superman gets his power from the fact that the Earth's sun radiates different energy wavelengths than Krypton's sun. Goku, on the other hand, would fight at equal levels (adjusted for gravitation) in any system. Of course, Goku would want to challenge himself by taking Superman on where the Man of Steel was strongest (as there would be no other reason for him to even fight Superman than the challenge - it's not like he'd be defending anyone from the Ultimate Boy Scout).
I was with a girl that posed this question to me once and swapped Vegeta in for Goku for that very reason, it's easier to come up with a "why".
But regardless of which Saiyan was in the battle, I usually sided with Superman. We know from evidence shown to us that even the most powerful of Saiyans can't survive (a) in a vacuum or (b) direct contact with the sun. Both are things that Superman has no problem with which gives him an advantage if it's a "fight to save the world" kind of fight. Superman's capable (depending on the writer) of kicking his heat vision up that high if he needs to, albeit doing so usually drains him if he's not doing it in direct sunlight. It's like Bulbasaur's solar beam, it can be just as much a liability as an asset if the atmosphere isn't on his side. Superman also has (or at least had at one point, I don't know what abilities and limitations he has in the New 52) the ability to fly into the sun and over-charge his own power.
Meanwhile, Superman's most exploitable weaknesses are kryptonite, magic, and the rays of a red sun. Goku, or any Saiyan really, is unlikely to really capitalize on those weaknesses either because they don't have access to them or just want to fight him at his strongest. All three are really wonky and inconsistent about how badly they effect him, but assuming the worst case of any of 'em it could amount to an instant victory for his opponent.
The more I think about it, though, if it were a "just dicking around" kind of battle (not out of character for Goku or Superman, really) I think that might be more likely to go Goku's way. In that case Goku has a distinct advantage of being aware of his opponent's limits and strength before the battle starts (since he can sense that stuff) and he'll know exactly how hard he can hit. While Superman is used to the "world of cardboard" problem and will only push himself as far as he knows it's safe to push. Superman would always be striking with just under the amount of power he probably could use... meanwhile, I don't think Goku even holds back when he's throwing punches at his children.
So I guess that would be my answer. No stakes: Could go either way, but I lean Goku. High Stakes End of the World kinda battle: I lean Superman all the way, unless his opponent has both the cunning and the means to "cheat" by exploiting his weaknesses.