Maybe this is a fresh perspective, from someone who has ignored consoles for 8 years:
As far as i can tell, when i last looked at Nintendo consoles they were the Wii, with a crap gimmick and almost universally panned games lineup. Now i look at it and it is considered to be beside/close to Sony as the dominant provider in the consoles market, renowned for great titles and even a revolutionary one in Breath of the Wind... And i don't even know that much about this stuff.
Let's look at this:
90s generation market dominance:
I dunno, en par with Sony? Ahead?
00s market dominance:
Behind ps2 and far behind xbox, then once more behind ps3 and xbox 360
10-15s market dominance:
Behind ps3 and xbox 360, then considered to be above the xbox at least.
I reckon this latest generation has seen Nintendo regain its rightful place in the consoles market. As such i think you have to say it's either the 90s or indeed this generation.
I guess, all things considered, you'd have to say the 90s, and I'm basing a lot of that guesstimate off their international success with Pokémon.
EDIT: OP I personally would say 00s, because Wind Waker, Metroid Prime, SSB:M and the like we the best console games I'd played in my life up to that point. Arguably Wind Waker and Metroid Prime retain that position.