Tough choice.
MC5 was the classic version of Detroit garage rock, heavier than the Amboy Dukes or The Frost. But I don't think that, musically-speaking, their albums went beyond the garage (even though they actually walked the walk and were truly a subversive group of political revolutionaries far beyond the posing of San Francisco bands of the time). They were a band that could literally kick your ass, and not just musically. And if you've ever seen photos of the band wielding rifles and machine guns, let me tell you, those weren't just stage props.
But Iggy and the Stooges I think transcended the notion of proto-punk garage rock. Certainly, Iggy was just as crazy as the MC5 (and there are numerous pictures of him bleeding all over the stage), but The Stooges music was much more anti-social and nihilist compared to the MC5's revolutionary protests and demands for social change, and that inward violence seemed to usher in the same attitude in the punk scene of the mid-70s. So, I'd wager a guess that the Stooges' music was far more influential in that regard.
That being said, having come from Detroit, I never could quite figure out what was the big deal about New York and London punks perpetrating an attitude that had already been done with far more violence an authenticity in Detroit in the late 60s.
I guess I'll choose The Stooges, because they had more consistency from album to album than the MC5 did.