Definitevely SNES.
Favourite games, in no particular order:

Megaman X

Super Metroid

Yoshi's Island

Super Mario Kart

Star Fox

Honorable mentions: Chrono Trigger, Actraiser 1 & 2, TMNT Turtles in Time.

90s Nintendo was simply better, even though Nintendo is still quite great today, look at the 90s and they had a top Game of The Year candidate (if not the flat out winner, like a very close runner up) like every year, whereas Switch era really can't boast that.

1990 - Super Mario Bros. 3 (probable winner of GOTY)
1991 - Super Mario World (runner up, probably Sonic wins)
1992 - Legend of Zelda: Link to the Past (probably SF2 wins, but this would be runner up)
1993 - Star Fox (probable runner up, Mortal Kombat I'm guessing wins)
1994 - Donkey Kong Country (runner up Final Fantasy III or Super Metroid)
1995 - Yoshi's Island or DKC2
1996 - Super Mario 64
1997 - GoldenEye
1998 - Zelda: Ocarina of Time
1999 - First year they probably don't have one (DK64 doesn't measure up), though this is the year Pokemon turned into a phenom in the West
2000 - Zelda: Majora's Mask and Perfect Dark

If you look at the last 10 years, Zelda: BOTW wins GOTY for 2017 for sure (Mario Odyssey even being runner up), but they haven't really had a GOTY contender on Switch probably since then, whereas during the NES and SNES era you could see it was a yearly occurrence.

NES and SNES also had legit 3rd party games (usually even exclusive) that were legendary titles, things like Megaman 1/2/3, Contra/Super C, Final Fantasy VI, Chrono Trigger, Street Fighter 2, etc.

People who didn't grow up in the 80s/90s or weren't old enough missed that, that was the really golden era of Nintendo dominance, not just market share but their power as an overall publisher. You will never see the type of run Nintendo had as a publisher from 1985-2000 probably ever again, because 85 GOTY would certainly be Super Mario Bros, 1986 would be Legend of Zelda, 1987 probably goes to Megaman 2 or something with Punch-Out! as runner up, 1988 would have Super Mario Bros. 2 up there but maybe not the outright winner, 1989 would likely be Tetris. So from 1985-2000 the only years where I don't think they had the GOTY or a game that was very close to winning would be 1987 maybe and 1999 and even 1999, Pokemon Yellow probably deserves to be up there as it was a huge hit for Nintendo and explosion of Pokemon in the West. 

Dragon Quest XI S is old-school with some pretty modern refinements. Shin Megami Tensei V and Tokyo Mirage Sessions (available on both Wii U and Switch) might scratch the itch as well. Octopath Traveler and Triangle Strategy. Wasteland 2 hearkens back to the era of isometric CRPGs, and the original game was a sort of precursor to Fallout. 

The SNES had tons of sports games though, it basically had from 1992 onwards everything the Genesis did EA wise (Madden, NHL, NBA Live, FIFA were big staples on the SNES for lots of people) but there were also some pretty darn good Nintendo published sports games like Super Tennis, NCAA Basketball (this is actually really the modern precursor to games like NBA 2K as it was basically like 3D basketball), and the Ken Griffey Jr. MLB baseball games were very popular on the SNES also. 

There were other decent 3rd party sports titles too like Tecmo NBA Basketball and Konami's soccer/football games. The SNES was actually probably the last Nintendo system that got basically all the main line up to date installments of major sports titles, sadly since then it hasn't been that way. NBA Jam (huge during the 16-bit era) was also better on the SNES (higher color pallette for better arcade ports). 

For sports games, I think the SNES is the best Nintendo system probably quite easily. Sadly on Switch you have wholesale IP like Madden NFL and NHL that aren't even on the system for one lousy installment. 

EA never really got along with Nintendo, in part because they couldn't control Nintendo the way they did with Sega. I read an interview a long time ago, with Bing Gordon, who was an EA executive in the early 90s, about how they more or less twisted Sega's arms into giving EA a special licensing deal with Madden 92, which is why EA Genesis games came on those big cartridges with the yellow tabs. They basically threatened to release Madden 92 as an unlicensed Genesis game and show it independently at CES 91 if Sega refused their terms. Gordon also mentioned that if Sega had really wanted to, they could have sabotaged an unlicensed Madden 92. 

These days, it's kind of funny to see the Switch version of MLB The Show 22 with a PlayStation logo on the front cover.

But most EA titles were on the SNES, which is really actually the last time that happened. 

I believe SNES got FIFA later (in 1994) whereas Genesis got it in very late 1993, but both systems had FIFA 95 for example. The SNES got Bulls Vs. Blazers 

I played a shit ton of NBA Live 95 and 96 on my SNES, same with various NHL games (NHL '94, NHL '95, etc.). 

If anything it's actually kinda funny that Sony aped the Ken Griffey Jr. endorsement for MLB The Show, because the Ken Griffey Jr. games were synonmous with Nintendo systems in the 90s. 

Gamecube.
At the time I felt it was extremely unique vs any other console I'd ever seen. The controller was the biggest deal. Not only did it fit perfectly in my hands, but everything about it was so ergonomic, except for the camera stick, which was still good enough. After long binge gaming sessions it was like I never had a controller in my hands the whole time.

The NES and SNES were worth the price of paid just for 3rd party games alone, that's kind of the difference with those two systems and everything that came after. Even if Nintendo never made a NES or SNES game, you'd have

NES: Megaman 1/2/3/4, Castlevania 1/2, Ghouls N' Ghosts, Contra, Super C, Metal Gear, Final Fantasy, Dragon Quest, Ninja Turtles, Ninja Turtles 2: Arcade Game, Double Dragon II, Wizards & Warriors, River City Ransom, Ninja Gaiden, Rad Racer, Tecmo Bowl, Duck Tales, Blaster Master, Batman, Battletoads, Baseball Stars 1/2, Blades of Steel

That alone IMO made the system better than the Sega Master System.

SNES: Final Fantasy V and VI, Street Fighter 2, SF2 Turbo, SSF2, Chrono Trigger, Actraiser, Megaman X/X2, Contra 3, Super Ghouls N' Ghosts, Breath Of Fire, Aladdin, The Lion King, NHL '94, NBA Live '95, Mortal Kombat 2, Secret of Mana, Super Bomberman, Super Star Wars/Empire/Jedi, NBA Jam, Castlevania IV, Earthworm Jim 2, Harvest Moon,
Ninja Turtles: In Time, Fatal Fury 2, DOOM, etc. (not even including non-Nintendo developed games like DKC 1/2/3, Uniracers, Star Fox, Super Mario RPG, NCAA Basketball, etc. here).

I'd buy that system too.

At the rate it is going, I feel like the Switch has a good shot at taking the throne by the time it finishes its run.

From first party gems like BOTW, Mario Odyssey, Metroid Dread, Kirby and the Forgotten Land, Xenoblade 2, and Splatoon 2, to great third party additions like Monster Hunter Rise, Witcher 3, Hellblade, Doom 2016/Eternal, Ori 1 & 2, Dusk, 13 Sentinels, etc, it's already built up a formidable catalog.

Once future additions like Xenoblade 3, Splatoon 3, BOTW's sequel, Bayonetta 3, etc arrive, it should have a real chance of dethroning the SNES in my book.

The switch just edging out the SNES. It’s essentially what the Wii should’ve been.
Plus. I thoroughly enjoy the split controller. I could lay in any position I deem comfortable.