Several points to consider:
1. We believe the gatekeeper is the oldest of the senior council, since he took down the Abdul Alhazred in 730 AD, according to WoJ. Also according to WoJ, the path to the gatekeepers personal demesne involve briefly walking on the moon, so we can assume wizards made it to the moon long before the rest of mankind did. If that is possible, I see no reason why the white council wouldn't be in contact with the America's before Columbus.
2. In the way way back, there were a lot really bad things running around. Way more than now - think of all the things locked away in Demonreach and by the Ventori helping the world forget them. There probably weren't that many more good things though, since why would we lock those things away? Maybe there was more direct intervention from various human pantheons, but even most of those are at least 50% evil (or have an evil opposite like the Jotuns). So Wizards back then might have been much more active in fighting for humanity than they are now, and a lot less worried about policing themselves.
3. Certain areas may have had less wizards per population that others. The Aztec/Incan region seems to have been ruled by the Red Court at the discovery of America. I see no reason why they would encourage/allow humans in their care to become wizards, and probably rooted out those with potential, leading to a very low wizard population in at least half of the new world.
4. Excepting certain powers intervening (ala red court in Mesoamerica) the population of wizards should probably be reflective of human populations, so it certainly does seem that the council is horribly western in leadership, considering that about 60% of the world population lives in Asia. And considering the references Harry has made about their locations, etc. it seems it has probably always been European dominated, which seems wrong unless there is a similar reduction in Asian wizard populations for some reason (hunted by jade court, etc.)
5. I do wonder though, back in the day before world exploration, it seems like it might have been relatively easy for the wizards to find each other with divination sources and paths in the NN, but it seems like communication would have been a total beast. There doesn't appear to be any magic way to learn languages (else Harry would be better at Latin) short of putting a demon in your head, and while it might have been easy to find a path to the America's through the NN, when they come out communication would be a bitch, and not what most people do for fun. I've got to think there has to be more value to being part of the Council or more punishment for breaking rules, else there is no way the world's wizards would have joined up like they appear to have done.