Yes, Eli is better than Peyton Manning and here are some simple reasons why.
1) He has played against much tougher opponents than Peyton during his time in the NFL. The NFC East has been the powerhouse conference over the past 3 years and Eli has only gotten better. Peyton has played against two EXPANSION TEAMS (Jaguars 1995, Texans 2002) and a Titans team who until last year we not that good and now that the Titans, Texans and Jaguars are starting to become more competitive, Peyton's numbers have started to slide (hint, hint)
2) Just compare both of there super bowl appearances. Eli got there in his 4th season. Just 3 years ago, ESPN analyst were wondering if Peyton ever could beat the Patriots and win the "big one". Eli played with a much less talented New York Giants team and played 3 straight road games against Tampa Bay, a strong Dallas team, and Green Bay on Lambeau Field with Brett Farve opposing him. Peyton on the other hand played Kansas City, Baltimore, and just squeaked past New England 38-34, and by the way, all those games were in the comfortable RCA Dome. Then the Colts finally got there and who did they face, the Chicago Bears ...... nothing else needs to be said.
3) While Peyton has had a free ride from the press in nice, media siberia Indianapolis, Eli has had to endure people wanting him traded, released, and everything else you can think of. Eli has had the New York Media hounding him ever since people found out that he was actually Peyton's little bro and now that the little bro has surpassed the big bro its not fun anymore and the media still holds Eli down when compared to Peyton.
So finally, don't get me wrong, Peyton Manning is one of the greatest quarterbacks to ever play on an NFL field and a future hall of famer. He probably will break of the records before he is done. Just dont be surprised if he records only stand for a few years because his younger bro has broken them.