Both QBs had brilliant coaches and schemes, although Brady plays in a time where the QB is FAR more protected (him in particular), so his stats have seen a boost because of that. The fact that Montana never threw an interception in four Super Bowls is ludicrous, though. Montana and Brady have both had plenty of clutch moments both in the playoffs, regular season, and Super Bowl. Montana had more dominant wins in his Super Bowls, whereas Brady has won them by 3, 3, 3, and 4. Two via last second FG and one by last second defensive miracle. The scandals against Brady don't help, either.
I tend to lean Brady over Montana because he's done more with less talent around him, but you can pretty much interchange them. Second half of Montana's career is fairly disqualifying to me.
Leaving out Manning was a nice touch.