Hmmm.
Both were groundbreaking for the superhero genre. Both showed that colorful, optimistic superheroes were relevant. You'd have to break it down piece by piece.
Christopher Reeve vs. Tobey Maguire: I feel like both actors embodied their respective characters perfectly. But we've now seen three actors on the big screen portray Spidey and all three have been received fairly well (I know everyone hates the ASM movies but Garfield himself has received a good share of praise), while Reeve is still the definitive Superman (and I say that as someone who really likes Henry Cavill). So I have to give the edge to Reeve.
Margot Kidder vs. Kirsten Dunst: Really no competition here. Kidder was a perfect Lois Lane in Superman. Yeah, the chain smoking was gross and the "Can you read my mind?" scene was cheesy as hell but she still nailed it. Dunst was okay and looked like the perfect MJ (at least in the first movie) but I always found her performance kinda flat.
Gene Hackman vs. Willem Dafoe: This is a tough one. I have issues with both villains; Hackman's Lex, while certainly more threatening and ruthless here than in the sequels, was nevertheless still campy. I especially had a problem with the stupid wigs. Seriously Gene; you've always had bad hair anyway. It wouldn't have killed you to shave your head for a role. And Dafoe, at least as the Goblin, always came off a little TOO corny with that stupid laugh. He was better in the scenes where he was just Norman Osborn though. But then there's that awful Power Rangers costume they gave him. If they had gone the prosthetic makeup route instead, it would have been so much better, IMO. Especially since Dafoe practically looks like the Goblin in real life. I'll call this one a draw.
Costume: No question here; Spidey wins hands down. But the technology to create an amazing suit was there in 2002; not so much in 1978. Still, that suit was a thing of beauty and it's still my favorite Spider-Man suit.
Script: Both have fairly simple, straightforward origin stories. But the Pa Kent death and funeral scenes in Superman actually made me cry so I have to give the edge to Superman.
Score: John Williams' themes are powerful, moving and iconic. Elfman's score... just felt like Batman/Edward Scissorhands/Everything else he's ever done. Superman wins this easily.
Direction: Another tough call; Richard Donner created the template for the modern superhero film, while Sam Raimi revitalized the genre. But I have to give a slight edge to Donner.
So all in all, Superman wins it for me. But Spidey is also really good. Now, if we were talking Superman II versus Spider-Man 2, Spidey would win hands down.