Goldeneye started the madness, yes. I would say the best 64 shooter was definitely perfect dark. Not so much for the single player(it sucked in my opinion). The multiplaye on the other hand was a gem. I can remember spending countless hours each day with 3 of my friends playing it.
What are you looking for? I agree with others by saying Goldeneye put console shooters on the map. Half-Life/CS has always been top for PCs. Tom Clancy games have always been true to their tactical shooter genre, while Call of Duty has been the best for historical shooters. Halo advanced the shooter genre by adding a great storyline and immense multiplayer. Could you choose one to be the best?
Personally, I've put more hours into Goldeneye and Halo1/2/3 than any other shooter, so I'd have to say one of those.