At first I was inclined to say Superman, because I think he's pretty much indestructible and Goku would only be able to win if he would be able to get his hands on some kryptonite. Furthermore, Goku has proven time and again that he can die.
But then again, if I look at what feats both guys are capable of, it seems Goku (towards the end of the series) is a lot stronger than Superman. Goku should be able to blow up a planet with the blink of an eye, and I don't see Superman doing that.
From the looks of it, I don't think Superman would pose much more of a threat to Goku than a human would. He's just harder to kill. And if Lex Luthor can get his hands on kryptonite, I'm sure Goku will find a way as well.