It's a tough choice between SNES and N64, both have a lot of good games that still hold up. It depends on what types of games you like.
The Super NES has a wide variety of great games in almost every genre imaginable. You've of course got your staples like the Mario games, Donkey Kong Country, and Zelda: Link to the Past, as well as other Nintendo greats like Super Metroid, Kirby Superstar, and more. There are some good puzzle to be had, too. There's a Tetris and Dr. Mario combo cart that gives you the two historic games in one, and there are games like Tetris Attack and Wario's Woods that are even more involving by having you line up specific colours (I'm a fan of SNES puzzlers, can you tell?). There's lots of RPGs of course, too many to even start naming.
Be forewarned however, that, of the four choices you mentioned, the SNES would be the most expensive one to build a collection. A lot of its best games (especially its RPGs) didn't sell very well, and are now highly sought-after, resulting in some relative expensive prices.
In contrast, the Nintendo 64 is a relative inexpensive system on which to build a collection. Though it lacks in a few genres, most notably RPGs and fighters. Well, there are quite a lot of fighters, but I haven't heard good things about any of them. I can't say I've played them myself (yet...), so I can't vouch if that's true, because I don't like fighters myself. Except Super Smash Brothers of course, which is a great game that still holds up. There are a handful of RPGs and none of them are anything special. Paper Mario is the only one worthwhile, though some enjoy Ogre Battle 64. It ain't cheap.
But the genres it does have, it does well. Platformers would probably be number one. And don't just stick will the well-known ones like Super Mario 64 and Banjo-Kazooie either! Overlooked gems like Rocket: Robot on Wheels, Glover, and Conker's Bad Fur Day are not to be missed. And there are some like Starshot: Space Circus Fever which can be enjoyable if you overlook theirs flaws. Beyond that, the system has quite a few fun shooters. There's the obvious Perfect Dark and Goldeneye. But when I want some straight-up shooty shooty, I go for Doom 64, Quake II, or even something like BattleTanx. There aren't many puzzlers for the system, but there are still some worthwhile ones. Tetrisphere remains the single greatest puzzle game ever created, not just 3D, but period. Charlie Blast's Territory is a "block-moving" sort of game where you have to push every bomb together to be denoted all at once, there's some clever puzzles in that little game with the stupid name.
Anyways... yeah. I could go on and on about the N64, but I won't. Though if you ever want a more in-depth opinion on an SNES or N64 game, feel free to ask me.