There is more to being a QB then just stats. There was no betterQB at manging the game and the clock then Joe Montana. He didn't need huge stats, or a lazor arm like Marino or Manning. He made great desicions and won games, and when it all boils down to it thats what matters the most. Sure he had a great offense, but so did Manning, and Marino(apart from a shitty running game). Marino had a great offensive line that protected him, and two pro bowl level wide outs. Neither were as good of desicion makers as Montana was. I find it funny the one stat you fail to look at when talking about Montana is his passer rating and his interceptions.
Favre started nearly a 100 games more then Montana, of course he's going to have better passing stats like passing yards, passing TD's and such. What he doesn't have Montana beat in is passer rating, superbowls, awards and accomplishments, interception/touchdown ratio, interception %, and completion %.