I love the N64, but Gamecube had a better library hands down. You could even play Ocarina and Majoras on GCN and it had MGS, Skies of Arcadia, Melee, Prime 1 + 2...
If I were to rank games individually, i would have a lot of n64 games sitting in the top, but looking at it as a whole, GCN brought a lot more to the table.
For me the better first party lineup + Rare in its prime gives N64 the win. GC did have better third party support, but the main draw of a Nintendo console for me is, well, the Nintendo games.
Rogue Squadron II was always the Gamecube title that I thought was most impressive on the console and Factor 5 even hand assembled some of the code to optimise it as much as possible or so an article I read claimed. It just looked fantastic and performed like a real high end arcade machine of the time. Amazing. I loved Metroid Prime but the graphics weren't very realistic with big blocks of colour and minimal texturing and as much as I loved windwaker visually it was more about the amazing art style. However Rogue Squadron looked better than any Xbox space games and you wondered if the xbox could pull it off to the same standard but then Gran Turismo at 1920x1080i on ps2 also looks very impressive. I do think however that the Xbox could easily achieve that and had quite a few 1080i games.
Gran Turismo 4 on PS2 wasn't native 1080i. Digital Foundry says it runs at 632x448. Still, it did look very impressive for the hardware, yes.
I don't recall Prime having "minimal texturing" though.
At the same time though, I wouldn't say it's one of the absolute best looking GC games; it's sequel looks significantly better, as do games like Rogue Squadron 2 + 3, Resident Evil 4, etc.