I never had a SNES when it was supported with games, so I'm naturally leaning towards the N64, but for the most part, I'd say that all Nintendo properties that made the jump from SNES to N64 are better on N64.
In detail though, I'd say the following are better without any caveats:
- F-Zero
- Star Fox
- Mario Kart
- The Legend of Zelda
- Yoshi
Now, I don't think I need to elaborate on WHY I think the first three are better - Mode 7 looks nifty, but even the N64's rudimentary 3D graphics give both F-Zero X and Mario Kart 64 a solid edge over the SNES versions. The same goes for Star Fox - the SuperFX chip is a really cool piece of tech, but the rendering capabilities and the controls of SF64 make it a much more playable experience in my book. With Zelda, I like ALttP a lot, but for one, it's one game against two, for two, one of these two is Majora's Mask, and for three, I think Zelda's 3D entries are often better than the 2D entries - the combat is more refined, the third dimension adds some nice exploration and to the puzzles and the presentation in both OoT and MM is just stellar. And with Yoshi there's one deciding factor: No Baby Mario.
The following are about even:
... and I think this boils down to the fact that both of these games respectively are very different. Super Mario World is a traditional platformer where the goal is to get through the level, Super Mario 64 focuses more on exploration and puzzle solving. So this is more of a "which flavour do you prefer" question than a question of "which is actually better"
And this last one comes with a caveat:
I don't dislike Donkey Kong Country... but my preferences when it comes to platformers make me enjoy DK64 more, as bloated as it occasionally can be.
And I don't have an opinion on Paper Mario vs. Legend of the Seven Stars because I haven't played the latter.