The Wii did not have the best first party games. Most of their first party games were flawed besides Mario Galaxy's. Metroid sucked, Zelda sucked, Mario Kart sucked, Animal Crossing sucked, no F-zero, it did have a solid Wario Ware and a pretty wicked Rhythm Heaven, as well as Excite Truck. Third party support was mixed, but definitely not their best third party support since SNES.
SNES remains their best console.
N64 had their best first party titles post-SNES, and also their best third party lineup post-SNES.

The only first party titles that still reign supreme are Super Mario 64 and Star Fox 64. Everything else is a toss up and debatable.
Ocarina of Time and Majora's Mask aren't really debatable. Also, Sin and Punishment. Including Paper Mario, which I'm not even a massive fan of, Kirby 64, Wave Race, Pokemon Snap, it's a no contest.
Third party, they had Goemon, Mischief Makers, WCW No Mercy, Harvest Moon 64, Ogre Battle.
Ultimately though, picking a best Nintendo system post-SNES is like picking which turd was the best. They were all lopsided highly flawed systems, but in hindsight, the N64 had the most going for it in terms of exclusives, innovation, and Nintendo giving a shit.
But if we're including handhelds, Nintendo's actual best system post-SNES is obviously the DS.
I'd say it's their best system period including consoles, although that has virtually nothing to do with Nintendo first party.