OoT is the objectively better game, but my personal favorite has got to be Banjo-Kazooie. It has so much personality, a fantastic OST, incredibly intelligent game design, fun characters...I played every save file to 100% completion.
Mario 64 is an important title -- not as a game, but what it did for video games as a whole, and I believe deserves an honorable mention here.
My favorite wacky title from N64 would have to be Mischief Makers. I'd be all over a remake/port/remaster soooo hard.
Love playing oldies, from consoles and PC, but very few N64 games hold up these days, played as back then, imo. Mario 64, OoT and similar caliber Nintendo games do though. Hard to pick just one given their quality but the choices aren't that numerous tbh.