Ultimately I think it's just too hard to compare Montana/Brady. Totally different eras, you can make a reasonable case for either one of them.
I never get ceased to be amazed how Brady was just a forgotten 6th round pick though. If he didn't play under Belichick's regime would he have had this success? I mean back in the day the Browns fans all hated Belichick for cutting Kosar since his skills didn't fit his coaching.