Admiral Karl Donitz. Though I don't think he was a Nazi.
From what I understand, he stopped Hitler's inspections of his crew to weed out Jews. He protected his crew from the Nazis and behaved in a reasonably honorable fashion given the circumstances.
I'm trying to think of individual sub commanders. Most of them were telegenic guys who wound up as folk heros back in Germany. Two Officers were a big deal if my memory serves right. One had blond hair and a movie star attitude, and one was just a kick ass Officer.
Arioch7 out.
Right. Karl Donitz. And he wasn't a Nazi - he hated the Nazis.