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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.

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, MK64 has a long and steep learning curve and for that reason is more fun for high skilled players.
NK64 on the other hand stands out 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 games, but MK64 is still the most durable game for local multiplayer (in fact we eneded up playing it 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.