That seems like an awfully big number, Unless there wasn't that many to begin with. Which brings another question to mind. How many Native Americans were around when European contact happened?
I read something about trade routes between the different tribes contributing to Pre-Columbian depopulation but nothing concrete and I wasn't sure where to look if that was actually a case.
AFAIK the most currently accepted theory of population decline in the early post-Columbus Americas was the introduction of foreign disease by European settlers. Native populations had immune systems that had never been introduced to these pathogens and so were defenceless to their effects.
Population estimates of the pre-Columbian Americas range from as high as 112 million to as low as 8 million. By 1650 the native population had declined to 6 million. The 90% statistic is something that I've seen touted often and it may very well be true. But we can't know for sure how many people actually lived across the Americas at the time.
Sources:
William M. Denevan. (1992). The Native Population of the Americas in 1492.
Noble David Cook. (1998). Born to Die.
There's always room for discussion, but perhaps the section Disease in the Americas in our FAQ will answer your inquiry.
Just to give you a snapshot of how. When smallpox broke out in 1862 there were 10,000 indians camped at ogdeon point just near victoria bc, Canada. They were from all of the coast tlinget, haida, tsimshian,kwakiutl and bella coolas among others. When smallpox broke out the city gave authorities the order to set fire to there camps. The people that were staying there had no choice but to go home to their communites they spread disease all the way to their respective communities. Source saltwater people by dave elliot sr