Mario 64 is rightly so one of the most cherished games in history, because it represented the "wow" factor of being the first big 3D adventure for a lot of people and more than anything represents a time in gaming where it felt like an uncharted frontier was opening up. And it did so in such a polished, incredibly inviting colorful package, it was like being wrapped in a warm blanket.
How many times have we heard people nostalgically look back and recount the first time they saw Mario 64 running at a Toys R' Us kiosk or something in those days of 1996/97 ... it's something one doesn't forget. I guess you could say Mario 64 is more a memorable game.
But GTA3 didn't exactly give birth to the idea of the violent, anti-hero/morally ambiguous hero ... but it certainly took it to another level. It also culturally brought cultural elements that were previously taboo in gaming, such as violent mafia/mob films and gangster rap into the gaming scene. It's also a pretty darn good game, even Mr. Miyamoto stated as much.
That said GTA3 also defines a lot about gaming that its critics use to define what the industry is all about -- GTA is the poster child for gaming being stereotyped for mindless violence in a lot of ways.