Super Mario 64, for me. Having replayed it recently, I am more convinced than ever of its greatness. It's one of those rare lightning-in-a-bottle games where the cutting-edge technology of the day mixed with total creative inspiration. The camera can be uncooperative at times, and the music tends to repeat toward the end, but the platforming is blissful and the sense of discovery, experimentation, and adventure is exhilarating.
Second place would go to Tomb Raider. It's not quite the equal to Super Mario 64, but I would argue it's damn close. A potent mix of visceral action and cerebral exploration & problem-solving.
I'd also like to give a shout-out to Donkey Kong Country 3. I know it's considered something of a black sheep in the DKC franchise, but I love its production design and expansive overworld. It feels like something of a "missing link" between Rare's tighter, linear SNES platformers and the more open-ended platform-adventure titles the studio would launch on N64.