In relation of its time, N64 games had way more impact in the industry and Nintendo itself, thanks to 3D gaming and a lot of new ideas. Basically every Mario 3D, Zelda, Mario Kart, Super Smash Bros, Mario Party, ... has been based for 20 years on thosee games that came on N64.
On the other hand, Wii had more games and more variety, but neither of its games, despite being absolutely more modern and polished were as memorable or surpassed the impact of any of the N64 ones. The fact that people got tired quickly of motion controls is another reason against Wii.
In my opinion N64, was the last time Nintendo tried to make revolutionary games that shooked the industry and made every other developers try to catch them or imitate what they were doing until Zelda BOTW came, impacting the industry again. Nintendo was only looking at the past until then instead of looking at the future.... so that's why my vote goes to N64, despite Wii games being more playable by today standars.
This poll shows too, that even for Nintendo fans and its loyal fanbase, if N64 wins or it's even tied with Wii, it proves that Wii was basically a fad. If half people now prefer a console that barely sold 30m against one that sold more then 3x more..., then it proves that the kind of people that bought that console were not there for N64 and were not for WiiU later either. People seems to remember more fondly what they played on N64 than on Wii, but i don't know, maybe it's just nostalgia....