I think the best two QBs are clearly Brady and Rodgers. Old Payton Manning belonged here, too.
I think tier two is basically Romo and Brees. If Eli can repeat his 2011 season then he might join this group.
The next group is Eli, Pig Pen, Rivers. These are all guys who are very good and have accomplished quite a bit over their careers but just are not quite consistenly as good.
Then the next tier is your other above average QBs who haven't yet shown they belong in higher tiers like Matt Ryan, Schaub, Vick, Stafford and Flacco. Stafford will jump a level if he can repeat his last season.
This is IMO a golden era of QBs we are witnessing. The sophistication of the offenses and the precision with which they throw the ball has entered another zone compared to the game I remember in the 80s and 90s. There are just so many really good ones now compared to back then. If you want to win in the NFL you need a good QB or you need to be good everywhere else (running, defense, special teams). If you lack a good QB or QB prospect you have to pay whatever price is necessary to get into position to draft one. That is why the Skins paid through the nose for RGIII and why the Colts wouldn't consider any offers for Luck.
Just thank your lucky stars that we got Romo. I was so happy to hear that he wants to play 6 more years as it gives us plenty of chance to build an elite team around him and win some Super Bowls before he retires. I actually think we have a good chance this year as last year's fatal flaws look to be remarkably improved thus far. If we can block the Giants well enough to put up 450 yards of offense with all their pass rushers healthy and playing then we're probably good enough upfront to play against anyone now. Likewise, we were able to defend against Eli and his WRs suggests our secondary is now good enough to compete against anyone out there.