Oh man. I have to say MKwii, though I really love it on the N64. Being able to use a wheel and having much better graphics just turns the table for me, but I love N64 much, so I say both:)
I interpret this question not as a question of which is better now, but which was better for it's time. A game like Mario Kart 64 is still fun to play with friends 10 years later, and most certainly is standing the test of time. I don't think I'll be able to say the same about Mario Kart Wii.