Those are the highest rated, but scores don't much too much at the end of the day - and most of those are Mario games, to boot, so "variety" is shot.
Personally, I've never played Splatoon, SM64 (I've played DS, which I still think is the pinnacle of 3D Mario, since it has very few truly-frustrating Stars to get, and despite being on the DS the graphical upgrade from N64 is very welcome as well), Galaxy 2 or Sunshine, or Ocarina of Time (I played 3D instead).
So...all I really could vote for is OoT, since there's not too much difference between N64 and 3DS there - unlike with SM64, the devs didn't add new dungeons or collectibles or anything, just streamlined things a bit.
My favourite Nintendo games would have to be Xenoblade Chronicles 2 (no duh), SM64DS, SM 3D Land, Twilight Princess HD, The Wind Waker HD.
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