Yes, in recent memory Eli is better. No one seems to realize that Eli has now won 2 Super Bowls with sub-par teams. Both of the times he's led the Giants to a Championship their defense was ranked 17th and 25th. Brady has never won a Super Bowl with a defense ranked less than 5th.
On top of that Brady has choked in his last 10-12 post season games.
Eli has won w/ D twice and last I checked if the "great" Welker holds onto that pass NE wins. Brady did what he could even after getting hurt.