OK turns out my stats were slightly off. Here's an expanded post, since I can't edit the previous one:
Since Brees joined the Saints in 2006, he beats Manning in most major statistical categories: completions, completion percentage, yards per attempt, and yards. Tied for TDs. QB rating is within one point. Over the past 2 years, Brees has almost 1000 more yards, 8 more TDs, and over half a yard more per attempt with the same number of INTs for a passer rating of 102.2 compared to Manning's 97.5.
The Saints have had the #1 offense 3 of those 4 years. The Colts haven't been top 5 in the past 2 years. Brees has thrown more TDs than Manning each of those years, except for this year where they're tied.
The only thing Manning has in that span that Brees doesn't is one Super Bowl win. Back in 2006.
It's not hard to argue that since Brees joined the Saints, and especially in the past 2 years, Brees has been a better QB than Manning. Also remember that before this year, Manning hadn't won a playoff game since 2006.