Warner was brought in to be a mentor for Eli. He was not expected to play the entire year (or maybe any of the year). As a matter of fact, they were 5-4 during his starts and 1-6 during Eli's. I know that is not a great record but it should be taken into consideration. Plus, take a look at the key players on the Giants that year: Tiki Barber, Amani Toomer, Ron Dayne, Jeremy Shockey. Granted, these players are not bad players, but when you are playing in such a competitive division, they are not going to get it done. Also, Warner was only on the Giants for 1 year. The Rams/Cardinals he was on multiple years, which makes a difference.
When Warner makes his move to the NFC West (St. Louis and Arizona) against lesser competition, you can see the damage that has been done.
Basically, you cannot factor Warner's stint with the Giants into the conversation about him being a top QB.