I think you would have to put QBs into a tier system. Peyton, Brady, Brees, and Rodgers are in the top tier.
I think Eli is in the second tier with guys like Rivers, Roethlisberger, and a load of others. It's tough to completely rank them all because where a QB is in his career makes a big difference. Matt Ryan could end up being top tier for instance. Joe Flacco and Matt Schaub are young in their careers. Michael Vick is obviously a freak of nature, but where does he rank since he's only been back in the league for two years. Also, I think people way overvalue a QB's team's performance in ranking them. The elite ones, to me, are the ones that are going to take their teams to the conference semifinals almost every year even if the supporting cast is average at best. Very few QBs can do that.
I don't think Eli is elite, but he's good for an NFL QB. For his sake though, I don't think it's bad if he thinks of himself as elite. QBs needs to have confidence. He's wrong, but it's good that he's that confident in himself.