It was apparently planned to be called as the Ultra 64 which would’ve been slightly more impressive in my opinion, but the N64 is fine too, I guess.
It was named so because it was based on a 64-bit processing unit, which was a pretty big deal at the time. Do you remember the Nintendo64 from back in the days of 2000s? It was released back in 1996, so that year people witnessed the birth of two phenomenal entities, N64 and myself! Jokes aside, N64 emulators for pc is genuinely a great gaming console, one of the legends.