Levi definitely belongs in that hallowed group of three. I don't think there's any doubt about that any longer. We were lucky to have him as long as we did, and it will be a long time before anyone else wears number 1.
That said, we all know that it's impossible to compare QBs across generations. Not only has the game changed, the preparation and coaching of quarterbacks is light years ahead of what it was in the 80s and early 90s. Imagine how much better of a passer Mitchell and even Delhomme would've been with modern QB camps in high school and college.
Furthermore, I doubt we'd have been able to land Mitchell nowadays. He'd have had his pick of schools willing to play him at QB.