There really are, but personally for me, the bigger the franchises and iterations that were on N64, or characters that started on N64, the better, Mario, Peach, and Bowser for Super Mario 64 (Peach's Castle N64, Princess Peach's Castle, or Rainbow Cruise as a stage), Donkey Kong, Diddy Kong, and King K. Rool for Donkey Kong 64 and Diddy Kong Racing (Kongo Jungle 64, Kongo Falls, and Jungle Japes), Young Link for both Ocarina of Time AND Majora's Mask (with Great Bay as his stage), Sheik and Ganondorf for Ocarina of Time (Hyrule Castle 64), Yoshi for Yoshi's Story (Yoshi's Story), Kirby and King Dedede for Kirby 64: The Crystal Shards (Dream Land 64 or Green Greens would work), Fox, Falco, and Wolf for Star Fox 64 (Corneria or Venom), Pikachu, Jigglypuff, Pokemon Trainer, Mewtwo, and even Pichu for Pokemon Stadium, Pokemon Snap, and Pokemon Stadium 2 (Saffron City and Pokemon Stadium), and Captain Falcon for F-Zero X (Big Blue).
I wouldn't count Link or Zelda since their incarnations in this game are based on Breath of the Wild and Link to the Past/Between Worlds, nor Samus since other than Smash, Metroid had no N64 incarnations which I distinctly remember or Villager since even though they did debut on N64, it was only in Japan and got remastered on GameCube, but I would count Wolf since he did debut on Star Fox 64. Mega Man did have Mega Man Legends on N64, but that wasn't exclusive to N64 and it was Mega Man Volnutt instead of the Mega Man in Smash, so I wouldn't count him either, and Pac-Man only had one game on N64 and it was Ms. Pac-Man Maze Madness which also wasn't exclusive and had Ms. Pac-Man in the lead role (they really should of made her an alt for Pac-Man, it would've been so simple). Sonic I would not include even though I get you were saying he had his 3D debut around the same time, just because it would be better to just have N64 reps. And even though Luigi, Wario, and Daisy did make appearance on the N64, they were mainly spin-offs.