MVP isn't exactly an objective measure of anything.
Manning was voted MVP, Brees was voted the Air Player of the Year. They each have an Offensive Player of the Year award, with Brees' award coming in 2008 and Manning's way back in 2004.
I'm not really sure if anyone could make a real case for Manning being the better QB in the past 2 years, especially this past year. In 2009 Brees had more TDs, a higher completion percentage, more yards per attempt, fewer interceptions, and a QB rating almost 10 full points above Manning.