If it's the article I've seen floating around the past couple days, it's an excerpt from Charles Mann's 1491, which I'd recommend you check out (I'd also recommend it even if the article you're talking about happens to be something else. Moral of the story: just read 1491). It's a good introduction to basic topics in the scholarship of Pre-Columbian history and how that scholarship has changed in recent years.

So, this 100 million figure is for the entirety of the Americas, North and South, and it is at the high end of current estimates. It may seem high, but for comparison, consider that the estimated population for Europe at the same time is around 90-100 million as well.

In 1492, Tenochtitlan (the Aztec capital, now the epicenter of Mexico City) was among the largest cities in the world, with a population of more than 200,000. Cuzco (the Inca capital) was perhaps half this size. Throughout Mesoamerica and the Andes, there were large cities with populations in the 10s of thousands. In total, perhaps a third of all people in the Americas lived in these two regions.

But these weren't the only places with large populations. Even in 1608, the population of Ivitachuco (the Apalachee capital, near modern day Tallahassee) was recorded by two different Spanish accounts as being between 30-36,000 people, though there is admittedly some debate if these accounts intended this estimate Ivitachuco proper or for the entire Apalachee "province." The population of Greater Coosa (the largest confirmed pre-Columbian polity north of Mexico, in terms of geography at least) had a population of at least 50,000 spread throughout the southern Appalachians; the capital of Coosa proper had a population of 5,000 or so. Communities between 2-5,000 are more typical among much of pre-Columbian Eastern Woodlands than behemoths like Ivitachuco (presumably) or its even older counter-part, Cahokia. These low-thousands populations synergized with the generally consensus-based mode of governance on that level. While why the population of an individual town might be relatively low, there could be a lot of them. Seventy-thousand Calusa here, a hundred thousand Iroquoians there. A hundred thousand Algonquians in New England; two hundred thousand Plaquemine Mississippians. By the time you're through, you've added another couple million people to the grand total just from the Eastern Woodlands. Then you do the same for other regions, like the American Southwest, the Pacific Northwest, the Caribbean (if de las Casas is right, you can add another 3 million just from Hispaniola), the Amazon (here's a relevant post I've made on what the Amazon was like at the time of European contact). If you're favoring the high-end reasonable estimates along the way, you'll ultimately get to that 100 million people.

As a final note, the idea that Native Americans were predominantly hunter-gatherers is erroneous. There were some societies that subsisted off non-agricultural means, some of which sustained relatively large populations with imperialistic ambitions (in the Eastern Woodlands, the Calusa are a prime example). Hunting and gathering societies were often an important part of the economic structure of their respective regions, trading their surplus meat, furs, wild plant resources, fish, etc., for agricultural products grown by neighboring societies. But for the most part, the majority of people lived in agricultural societies of various sizes and political shapes.