I think in the popular perception, there have been several shifts.When did Brady's momentum ebb? When he was injured for a year?
Pre-2006: Brady has rings, Manning has stats, edge: even
2006: Manning gets a ring, edge: Manning
2007: Brady sets TD record with Moss / Welker, makes another Super Bowl, edge: Brady
2008-09: Brady hurt, Manning two MVPs, Manning another Super Bowl, edge: Manning
2010-11: Brady second MVP, Manning misses a year, another Brady Super Bowl, edge: Brady
2012-13: comeback year for Manning, record-breaking year, another Super Bowl, edge: Manning
2014: Manning signs of decline, Brady fourth ring, edge: Brady
Each has had his proponents and detractors throughout, and each has been awesome forever so this is all a little bit silly, but I think this is how the popular perception has gone.