As a kid a played a lot of both. I personally owned a PS1 and CTR while a friend of mine had an N64 with Kart 64.
If I have to draw an honest comparison beetween the two, I'd say CTR stands out for better overall track design, more content and the single player campaign.
Both games had a great driving system and, while CTR is more balanced and polished, MK64 has a longer and steeper learning curve and for that reason is more fun overall for high skilled players.
NK64 stands out also for the item system (the best in the series so far) and for the battle mode (in a league of its own).
Overall I'd say CTR is the most polished and comprehensive game, but MK64 is still the most durable game for local multiplayer (in fact I eneded up playing it with my friends longer than CTR).
That said, MK has evolved a lot since then. So while I agree CTR is a great game and beats MK64 on many levels, the MK series has a whole is definetly superior. It's not even debatable for me.