Steve Young (although McMahon is right there).
I love all the others and some did things nobody else did (Ty-helaman, Boscoe - NC) but there's just no mistaking that Jim McMahon was the best ever at BYU. If you aren't old enough to remember watching him I feel bad for you. You should have been born sooner.
Also, I think Boscoe is generally underrated. He was also amazing and would have had a long nfl career except for injury.