Tough question, but an interesting one. If you look at it from the stand point of which team ended on a better note, it's definitely the Gophers. If you look at it strictly from an achievement standpoint, it's probably Iowa, even though they didn't even make it into the final 64. Even still, Iowa did make it to the NCAAs and the Gophers did not.
Having said that, with how badly Iowa struggled down the stretch, it makes for an interesting conversation. In the end, I voted for the Gophers because they finished on a high note while the Hawkeyes fell apart in the final month. In other words, its all about momentum heading into next year for me and right now, Minnesota has it while Iowa does not.
I guess the best analogy I could come up with is that Iowa's season looked eerily similar to last year for the Gophers (taking into account that the Gophers actually made the round of 64 and then actually won a game, neither of which Iowa did this year). Still, there were quite a few posters, myself included, that weren't exactly thrilled with how things turned out last season. And I happen to know Iowa fans were severely disappointed with how their year concluded.