Goku would Crush Superman

Madara would stand absolutely no chance.

Madara's best hope, as others have mentioned, would be to trap Goku in a genjutsu. In order for this to happen, he would need to make eye contact with Goku. There's the problem.

Goku does not need to see Madara to fight him effectively.

Among the many things Goku learned while training with Mr. Popo was the ability to sense ki, a sixth sense that was as sensitive (or more) than the normal five senses.

Madara's next-best bet would be to light Goku on fire with Amaterasu.

This would depend on Madara seeing Goku. While the shinobi of Naruto are certainly super-human, none of them achieve anything close to the speed and strength of the characters in Dragonball Z. Goku would likely simply be too fast for Madara to use such a technique. Even if Madara were to successfully capture Goku in a rinnegan technique or some such thing, Goku had the ability to teleport. It would be like fighting Minato, except thousands of times stronger, and with the ability to fly.

There is practically no other move that Madara knows (at least none that I know of) that could not be overcome with simple brute strength, ignoring Goku's other experience and battle sense. Dragonball Z's characters are pure power fantasies. It is unlikely any character in any other mythos, short of gods or fanfictions of Superman, can match Goku.