So games only made in-house, not games published and IP owned by Nintendo but developed by partners like, say, HAL Laboratory or Rare? Meaning no Earthbound, no Kirby, no 90s-era Donkey Kong Country, not even the first two Smash games?
If so, then that complicates things.
I still want to say it's a toss-up between the SNES and NES. The NES had more in terms of quantity, but some of Nintendo's output on the SNES was of high quality, even ignoring the better graphics. The NES had some games that are still fun to play, including the first three SMB games, Punch-Out, Duck Hunt, Star Tropics, and even a Nintendo-developed port of Tetris, plus ports of their early-to-mid 80s arcade games. However, the SNES had Super Mario World, A Link to the Past (vastly superior to the NES original), Super Metroid (same), F-Zero, Super Mario Kart, Super Mario All-Stars, and Yoshi's Island.
Hard to say where I'd rank the rest, but I'd put the N64, Wii U, and Switch above the GameCube and Wii.