GC > Wii > N64 > Wii U

I bet Switch will sit beween GC and Wii.

Gamecube and Wii were the best. It doesn't look like anyone else has mentioned that the Gamecube was the last Nintendo console with licensed sports titles that third parties actually expected anybody to play. The Wii would get dreadful versions of those types of games, the U quickly stopped getting any at all. Wii had all sorts of cool games made specifically for the system though, Boom Blox and No More Heroes as mentioned in the OP but also Zack & Wiki, Little King's Story and de Blob, among others. It also had real random shots in the dark that nobody remembers such as Deadly Creatures and Cursed Mountain. Your mileage may vary as to whether those games were that good but I love that they were even attempted. So I give Wii the edge because a lot of solid or interesting titles were made with that console in mind.

I largely skipped the 64 but I'm still confident in saying it was better than the U. Wii U barely got anything and what it did get was usually gimped in one way or another.

Agreed, mostly. I questioned whether things were actually improving when we first moved into 3D.  In hindsight, I see that gaming was going in the right direction.  But, at the time, I thought many of the 3D characters were terrible.  I especially disliked Virtua Fighter.  But, popular opinion seemed to be that it was amazing. 

Anyway, yeah.  Many (most?) games of that area basically suck, when played in 2017.  But, they were viewed through a much different lens back then.  

GCN > Wii > N64 > Wii U

The Wii's third party lineup is underrated.

Yeah, you had a lot of shovelware, but there were lots of quality titles too; Monster Hunter Tri, Goldeneye 007, COD MW/W@W/BO/MW3, Tatsunoko vs Capcom, No More Heroes 1 & 2, Red Steel 2, Sonic All Stars Racing, Sonic Colours, de Blob 1 & 2, Silent Hill Shattered Memories, Rayman Origins...

1. Gamecube
2. Wii- Ya it did not get ports of many of the major titles on PS360 but it got quite a few 3rd party exlusives
3. WiiU- Pretty bad, but N64 got even less support.
4. N64 (possibly greatest 1st/2nd party support of any console ever, but 3rd parties just did not show up)

Considering the Wii had backwards compatibility with gamecube... N64 > Wii > NES > Gamecube > Wii U.

Tough to say.. Wii had the most quantity of 3rd party games, but Gamecube probably had the best ones. It was actually one of my favorite Nintendo consoles for third party games outside SNES. And it's probably the only Nintendo console where I actually prefer more 3rd (and 2nd) party games than Nintendo ones..

Tales of Symphonia, Eternal Darkness, Phantasy Star Online, Sonic Adventure 2 Battle, Super Monkey Ball, Resident Evil series, Timesplitters 2, Soul Calibur 2, Tony Hawk 3, etc.. Some of these aren't just still my favorite Gamecube games but favorite GAMES period. 

N64 wasn't good for 3rd party but certainly great when talking 2nd party, as Rare back in the 90s were probably my favorite gaming company second only to Nintendo. 

Wii U? Bleh..

Gamecube is probably the one with the most 3rd party titles I've liked from those consoles (Tales of Symphonia, Phantasy Star Online, Gladius, TimeSplitter 2 &3 to list a few).

Going by number of third party games I actually bought (or got); N64 > GC > Wii > WiiU.

Though that's probably not really fair since I just have way more N64 games than I do WiiU games, about 50 for the former and like only 12 or something on WiiU.

Gamecube could probably have been much higher had I actually payed attention that gen.