Jordan never lost when he made it to the Finals. The only thing that disrupted him once the nineties began was his two retirements, other than that he was six for six.
Brady is not six for six. He's lost Super Bowls to the likes of Nick Foles and Eli Manning (twice!). He struggled mightily with those Denver teams, even after Peyton Manning was physically expired. Its not analogous to the Jordan years for a couple reasons. One, football is a different sport than basketball. Two, Tom Brady never had a self-imposed exile. Other teams have intruded on his dynasty with decent regularity, of those teams only one in the last twenty years was helmed by an expensive veteran quarterback. 2006 Colts.