I gather this is the source that is most cited for the 100 million figure http://www.oupcanada.com/catalog/9780195085570.html
Death counts are hard to establish because usually nobody cares about the people dying. For example the US does not keep numbers on indigenous deaths for countries like Iraq. The counting is left up to other entities which can take a while. It doesn't surprise me that over time the numbers get bigger and bigger basically because nobody has worked on it.
Looking at that source, I think the 100 million figure counts the entire North and South American continents. However, I think if you were to just count the Native population of what is the modern day USA prior to European conquest, than you're probably looking at a few million. It's worth keeping in mind though that concrete evidence for historical events can often be scarce and will also vary depending on the political opinions of the historian.
It's also important to put things in context. Almost all empires and great civilisations committed heinous crimes. That's often how empires are built. The Mongol conquests and invasions for instance is believed to have resulted in around 40 million deaths. The Ancient Egyptian civilisation was built on slave labour...etc.
