Those early runs when they were most dominant and won 3 championships in 4 years, Brady never threw 30 TDs or over 4000 yards in a season, never was an all pro and the offense didn't run thru him but thru the run game with Smith, Dillon & those guys.. His stats show it, his accolades show it and in general how those teams won (with defense) show that TB12 as we know him today wasn't much more than what Schaub was for us circa 2008-9...So you have to deduct off of TB12's greatness & add to BB's for that.
So I believe early on in their run BB was the more dominant force just b/c of how he ran his teams, but over time that eroded a bit to where towards the end of their run it evened out more. For me tho, i still give the edge to BB b/c The best thing Brady did for so long was be a good soldier and allow BB to run/control the team how a HC needs to. Had TB12 been more in the vein of a guy like Rodgers, TB12 is probably shipped out of there after 5-8 years & we're not having this convo.