I really liked the behemoth fight in CV64. It was so awesome, how the flesh burned away, and how it lost it's lower part and shot light-beams and stuff. Very cool. Besides that I can't remember a single boss that was noteworthy in any way in N64 games.
In CoD... Well, the Wyvern was cool, but other than that... Even Dracs 2nd was... totally unamusing.
Scv4 had great bosses like the Viper and the last stage before Drac being kind of a boss rush.