CiG
Approximately Infinite Universe
If I had to choose the best Rare game I would probably agree with Perfect Dark. My friends and I probably sunk more hours into that multiplayer than any console other game. After than it's hard to choose... Strictly on N64 I would say Banjo-Kazooie is second best, but if we include SNES I would probably rank Donkey Kong Country 2 as their second best game.
Rare had one hell of a run any way you look at it. Very consistent quality. It's too bad Microsoft bought them....
Hopefully Sea Of Thieves brings them back to their deserved glory.
If not, we have Yooka-Laylee and Lobodestroyo to make up for it.