Very tough question.
The NES had great games, but disqualifies itself due to it's crappy, flimsy hardware.
The SNES is a top contender, great games and great hardware.
The N64 was powerful, but held back by it's format. and the controller just looks weird.
The Gamecube had great games and a superb controller (and the best ABXY button layout ever. If that one ever gets updated with 2 Z triggers and buttons under the thumbsticks, it's gonna be the best controller yet again). Too bad it didn't help Nintendo, because the cube definitely was worth it - especially the Panasonic Q version.
The Wii is very divisive, but I liked it, just like many of the games on the console.
The Wii U is yet another console that failed at the consumers, but it's not all bad, really. Nintendo produced some of it's best games for the console, and the lack of AAA games meant it was a haven and heaven for indie games. Both later paid off with the Switch with successors and ports from Nintendo games as well as having a large Indie fanbase right from the start.
In the end, it's a duel between Gamecube and SNES, but the other consoles are not far behind. Due to how much I like the Gamecube controller, I'll choose the cube
The Nintendo eShop rating Thread: http://gamrconnect.vgchartz.com/thread.php?id=237454