Maybe. He is definitely a winner; but, then again, so is Big Ben and I would hesitate to qualify him as an "elite quarterback" while still maintaining that he could be viewed as approaching "elite player" status (if that makes any sense, whatsoever).
Namely, the total eggs he laid against Washington and Seattle.
I did look at QBR before posting that, and Eli did do fairly poorly. In the Giants two losses this season, Eli was 19th in week 1 against the Skins and 25th against the Seahawks. Those games you mentioned with Brady: 8th in the NFL against Buffalo, 16th against Dallas and 13th against New York. Also, Buffalo, NYGiants and Dallas are 5th, 7th and 11th in opposing passer rating, while Washington and Seattle are 20th and 22nd respectively. So, in effect, Tom Brady has ranged mediocre to decent against fairly stout pass defenses, while Eli has had two mediocre to bad games against bad pass D's.
Brees game against TB wasn't that bad, but his performance against STL was definitely inexcusable.
Just had a conversation today about whether Eli will get into the HoF or not. I think that if he wins a second ring, he'll make it in but I don't think he's at the level of some other current HoF type QBs (namely, his brother).
I voted no. The upper echelon consists of Rodgers, Brady, and Peyton, with a second tier having Brees, Rivers, Eli, Schaub, Big Ben, Stafford, and any others that I missed. There are quite a few in that second tier, but there is a huge gap IMO between the best and the rest (Brees is close, I think).