Tough to say.. I have nostalgia for both in different ways: N64 was my console growing up as a kid, Gamecube as a teen.
I'd have to say N64 for the multi - Goldeneye, Smash Bros, Mario Kart 64, Mario Party, etc..
Gamecube for the single player - Metroid Prime, Eternal Darkness, Tales of Symphonia, Pikmin