I think the SNES is Nintendo's weakest generation. It had good games, but they were just SNES sequels to their NES game (in a similar way, GameCube was the N64 part 2, Wii U was Wii part 2, GBA was GB pat 2, 3DS was DS part 2). I think the NES, N64, Wii , GB, and DS eras were really the most defining for Nintendo (jury is still out on Switch, but lot of retreading Wii U thus far).
For my money, N64 was peak Nintendo. Some of the greatest games of all time, where sequels were all reimagined in new, unique ways. Mario 64, Ocarina of time, Smash Bros, Mario Kart 64, Wave Race 64, 1080, F-Zero X, Majora's Mask, Pilot Wings 64, Pokémon Stadium, Pokémon Snap - pretty much the invention of modern Nintendo right there.
I think this is an inspired contrarian take.
My first reaction was - "N64? The console that was badged 'Project Reality', but actually could only do low poly and/or foggy worlds? The console with a small library with probably the worst third party games besides Virtual Boy?".
But consisering the argument further, it does have truth in it. Nintendo created genre defining mechanics in more games than one. It estblished the ways many franchises work in 3D. It was a truly creative time for them, even if their ideas were realised on a flawed platform.
In that sense, I feel the DS/Wii era was similarly productive and creative for them.
The amount of fresh gameplay ideas coming out of DS - from both Nintendo and third parties - was truly inspiring : Steel Diver (originally a DS unveiling demo), Wario Ware Touched, Super Mario 64 mini games, Ossu Takae Ouendan, Meteos, Nintendogs, Elektroplankton, Another Code, Professor Layton, Dr Kawashima's Brain Training, Daikasso! Band Brothers, Metroid Prime Hunters, Zoo Keeper, Feel the Magic... it really felt like the cambrian explosion of game play mechanics innovations at the time. While many if these mechanics proved gimmicky and didn't become genre defining innovations, many of these ideas can be traced to mobile games today.
Wii promised initially similar potential, which is why the controller trailer, without showing any gameplay, blew up to make Wii the biggest Nintendo thing ever. Regrettably, due to hardware shortcomings of the Wiimote, most of that potential was never realised satisfactorily, so Wii had little lasting impact in gameplay ideas.
So, if the criteria is "innovation", not "polish", I would say it's a toss up between N64 era and Wii/DS era.
Personally, Switch is peak Nintendo for me. It's almost like Nintendo telling me "man, thanks for being a fan, here's the console you've always wanted from us". The amount of great games I have played on Switch in less than two years is absurd, both first and third party. And the hybdrid concept of home & away has me allowed to really play them all, while I have missed them first time around. Zelda BotW, Mario Kart 8, ARMS, Splatoon 2 + Octo explansion, Super Mario Odyssey, Donkey Kong Tropical Freeze, Xenoblade 2 + Torna, Octopath Traveller, Mario + Rabbids, Hollow Knight, Super Meat Boy, Super Smash Bros Ultimate, Bayonetta 2, New Super Mario Bros Deluxe, Captain Toad, Hyrule Warriors., Pokemon Lets Go, Super Mario Party, Nintendo Labo, Kirby, Sushi Striker...
Switch is peak Nintendo in polished, fully realised game play, home and away.