Star Fox 64 looks a billion times better, plays smoother, has the famous voice acting (hilarious lines, yes - but infinitely quotable and relatively well-delivered), controls much better, has the great force feedback, the great shoot-em-up action (delivered with an addictive combo-mechanic), has more techniques to perform in flight, has the all-range mode (which I actually LOVED - felt like Independence Day when enemy battleships would fill the screen and it was you and your little team versus an army of doom), had fun multiplayer, had more levels, had more varied environments (and new vehicles to use as well - wish you could've used the Great Fox, though)...
Even though the SNES had better, more videogame-y awesome music, it's not like the SF64 soundtrack was the worst thing of all time. The mediocrity of the soundtrack doesn't hold down the significant improvements of virtually every other facet of the game.
SF64 wins.