I wrote a paper about this for a college class a while back. I'll try to summarize.
"Defense wins championships." - The Most Overused, Incorrect Quote Ever. The only two Super Bowls I've seen that quote ever prove true is the Ravens vs. Giants Super Bowl (that was painful to watch) and Bucs vs. Raiders Super Bowl.
Championships appear to be the way to rank a QB for most people (thus, the Brady 3, Peyton 1 argument). However, if that's the case, is Dan Marino worse than Brad Johnson, Trent Dilfer, or Phil Simms? And does that make Terry Bradshaw and Joe Montana better than Brady?
You can't compare the two based on Super Bowl success. The Patriots have had elite defenses going in their Super Bowl years, the Colts have never really ever been known for defense (ironically, their defense played better during the playoffs). You must compare them on their on-field achievements.
One thing you can compare are their best years. Peyton's 49 TD year and Brady's 50 TD year. Brady clearly had more touchdowns, but he favored Randy Moss for big plays and touchdowns (which is why he broke Jerry's record of 22). Peyton spread to all of his receivers (Harrison, Stokely, Wayne) as all of them caught 60+ receptions, 1,000+ yards, and 10+ TDs a piece, which has never been done by any other quarterback.
The "Brady won with no-name receivers" is one of the worst arguments I've ever heard. Manning didn't always have Harrison, Wayne, Gonzalez, and Clark. Manning helped shed light on his receivers because of his name. Before Dallas Clark, Marcus Pollard was Manning big name TE. Now, he struggles to even stay on rosters since he left Indy. Even before Pollard, there was Ken Dilger (who he made a pro-bowl TE). Brandon Stokely had his best years in Indy as well and was recognized as one of the best slot receivers in the game during his time with Peyton. Before Reggie Wayne it was Qadry Ismail.
It's the same with Brady, except Brady never had the name, so you never focused on their offensive players: Branch, Brown, and Givens. But, when Brady's name grew, you knew who they were. And the exact same thing happened when his receivers left: they became irrelevant. Branch became hot shit and went to Seattle and he's... not doing much. Givens... well, I don't know where he went and I don't think anyone really cares. Troy Brown stayed with the team and he's going to be loved for everything he did for that team because he's respectable. He's the oddball (more like lucky one) out of that equation. They both make their receivers so much better.
The arguments go on and on, but at the end of the day I give Manning a slight edge over Brady, but regardless you can't take away the impact that either of these men have made on the game. Manning, a 3-time MVP, 4-time All-NFL, 1-time Superbowl MVP and Brady, 1-time MVP, 1-time All-NFL, 2-time Super Bowl MVP. They are both remarkable quarterbacks.