Its not even close. Eli Manning played really well down the stretch of the regular season and in the playoffs the year the Giants won the Super Bowl, but he wasn't the main reason they won.
He's always remembered for somehow getting away from Patriots defenders on that famous toss-up, but David Tyree made the magical catch, and is the guy who really should get the bulk of the credit on that play. Then Eli tossed the eventual game-winner to Plaxico Burress, but the game didn't end until the Giants aggressive defensive line bull-rushed the Patriots into submission on the final drive of the game.
Peyton, on the other hand, won with a less impressive defense and has done so for most of his career. His defenses have always been solid, and sometimes really good, but I'd argue that none of them ever were as good as Eli's was that one year.
And even if you can say Eli had a lot to do with that title win, that still was the only year where he had things remotely together. He's been a pretty inconsistent player, otherwise, while Peyton has been the model of consistency and elite production in all facets for his entire career.