Big difference for me is that North Dakota and Minnesota have been a lot more consistent than Michigan. They won a lot of their NCAA championships in the 40's and 50's, then kinda fell off the map for the most part for decades. North Dakota and Minnesota both have had only a few short down periods in that time.
Also, I know this topic has been beaten to death for years, and I don't want to stir this debate up, but Ithink if you are going to look at the best programs of all-time, you have to at least give some weight to the hockey played prior to the NCAA era. And I'm not neccesarily saying this will mean as much to fans of other programs as it means to Gopher fans, but being the first program to win a championship with only US players and the only program to do it with in-state players (they did that twice) is kinda special.
If it were up to me, North Dakota would be my #1 (slight edge) and Minnesota my #2.