90% fatality due to novel diseases

The numbers always vary.  This is a recent estimate.  From Is a colonial-era drop in CO₂ tied to regrowing forests? by Howard Lee.  The subheading is Carbon dioxide dropped after colonial contact wiped out Native Americans.  

The article is obviously AGW oriented but it does have these numbers for pre and post contact America.

Scientists estimate that about 60 million people inhabited the Americas before European contact. There’s archaeological evidence for numerous cities and settlements, such as miles of now-overgrown urban sprawl that was recently mapped in Amazonian Ecuador, or the city of Cahokia in Illinois, which is estimated to have been larger than London was at that time, or Llanos de Mojos in Bolivia. The Spanish conquistador Francisco de Orellana also described seeing cities in the Amazon in 1542.

Even today in overgrown parts of the Amazon, vegetation carries the imprint of past occupation in an overabundance of cultivated species such as Brazil Nut trees.

A century after the first European contact, some 56 million people had died according to one widely cited estimate. “What we're looking at here is first contact, and [then] 100 years when 90 percent of the population, basically, dies,” said Professor Mark Maslin of University College London, who was not involved in King’s study. They succumbed to wave after wave of pandemics, as smallpox, measles, influenza, bubonic plague, malaria, diphtheria, typhus, and cholera spread through populations with no natural immunity. People who survived one disease outbreak died in the next. With too few people to work them, cities and farms were abandoned and overgrown.