I'll say it. Eli > Peyton. I don't like Eli, personally. I think he is a spoiled little baby who rode his brother's name to a great D1 school and then awards and a draft position that he didn't deserve (both Roethlisberger and Rivers are more talented than him and should've gone ahead of him). The **** he pulled with San Diego is beyond reproach. That being said, he is better than Peyton.
Peyton is a great statistical quarterback, he is great at breaking records, but he can't bring home titles. The only reason he even has one ring is because the Colts snuck into the Super Bowl in a year when the Patriots were crazy injured and the Steelers were suffering from a Super Bowl hangover. And even then, they still nearly lost both the divisional and conference championship rounds.
The Colts then went on to beat the single worst team to ever make it to a Super Bowl. Peyton got lucky. All the stars aligned perfectly and he STILL struggled in the 2006 playoffs.
I hate using this term, but it applies here: Peyton isn't clutch. Eli is. In the playoffs, Eli is just a different man than he is in the regular season. Peyton is the better regular season QB. But if it were a huge game or the season were on the line, I'd pick Eli every damn time. And for that reason, Eli is better than Peyton, IMO.