We don't really know how many indigenous people lived in North America pre-contact. I wrote about this here a few days ago, but one of the tricky things is that those population estimates rest on a lot of assumptions about morality caused by disease, enslaving and the other ills of colonialism and don't always account for the deliberate genoicde(s) of native Americans by colonial, state and federal governments across the continent.

(In that answer I used Mann's 1491 to discuss America north of the Rio Grande, but keep in mind that North America goes all the way down to Panama and includes the Caribbean.) u/drylaw posted a similar answer which also talks about the population numbers in what's now the U.S. and Canada, but doesn't address Mesoamerica or regions further south.

In terms of

if we are to assume that 100 million Native Americans lived on the continent and were ravaged by plague, where is the physical evidence? Where are the permanent cities and towns, where are the supercenters of trade and cultural exchange? Where are the mass burial grounds? The bone fields? Is there something I'm missing? Was the entire population centered in the central and south American empires where urbanization existed? How could they have higher populations that pre-little ice age Europe?

there's physical evidence of Native American presence in North America everywhere. Leaving aside the massive pyramids of stone that are dotted throughout Mesoamerica, and the stone cliff-dwelling structures in the Four Corners region of the United States, there are many earthworks left behind by the Mississippian and Hopewell cultures. The most obvious preserved urban (earthen) structure in the U.S. is Cahokia, near the present-day site of St. Louis, which may have supported a population up to 40,000 at its heyday. The answer I linked above from u/reedstilt goes into detail about the Hopewell astronomical observatory in Newark, Ohio:

The Hopewell, one of the most important cultural complexes of the Americas, were expert geometers, astronomers, and surveyors (to name just a few of their many talents we are able to detect after some 2200-1500 years). Their largest site is the Newark Earthworks. There are four features of particular note here: The Octagon, the Observatory Circle (connected to the Octagon), the Square, and the Great Circle.

The diameter of the Observatory Circle, 1054 feet (hereafter called an “OCD” – Observatory Circle Diameter), and fractions / multiples thereof are the basic units of measure employed by the Hopewell at this site and other Hopewell sites. The distance from the perimeter of the Observatory Circle to the center of the Octagon is one OCD, and the Octagon is itself constructed from squares of one OCD to a side. This video illustrates the relationship. The distance between the centers of the Observatory Circle and the Great Circle and between the centers of the Octagon and the Square are both six OCD.

Moving on to the Great Circle, it seems anomalous if you’re familiar with other Hopewell sites. They usually include a large circular feature with a diameter of one OCD. Why is the Great Circle so much larger? The relationship between the Square and the two Circles holds the key. The Square’s area is the same as the Observatory Circle’s, but its perimeter is the same as the Great Circle’s circumference. At the very least, the Hopewell seem to have understood pi quite well.

Swinging back around to the Observatory Circle and the Octagon, you might be wondering why the Observatory Circle is named the “Observatory” Circle anyway. It’s because the major axis of the Circle-Octagon complex aligns with the maximum northern moonrise, one of the eight lunar standstills. Other prominent components of the Octagon align with the other seven standstills. This was discovered in the 1980s when researchers were attempting to debunk the then-recently reported solar alignments found at Stonehenge. Any significantly complex site, they hypothesized, should have such alignments just by mere coincidence. To test their hypothesis they chose the Newark Earthworks, plotted it for solar alignments, and to their surprise came up empty. One of their students, rather offhandedly, suggested that they might look for lunar alignments, and then things started to snap into place.

Now, since they were hypothesizing that a complex site should have chance alignments there’s been some debate over whether the alignments were intended or whether the hypothesis was correct. Since then, analysis of the Newark site and others indicate that mere chance alignments are highly unlikely. Newark, Ohio isn’t the only place the Hopewell built a circle-octagon observatory. Another once existed in Chillicothe, Ohio, but has sadly been demolished. Based on land surveys of the area that show Chillicothe’s observatory, it’s major axis also aligns with one of the lunar standstills. The Hopewell seem to have been very interested in this 18.6 year lunar cycle for some reason.

If you're interested in reading more about this, our FAQ has some good posts on the topic.

To clarify a few points, the 100 million population estimate is usually in reference to the Americas as a whole, not just North America. It's also the high-end estimate. The low end estimates are closer to 50-60 million people in the Americas. In either case, about half that population is going to be concentrated in Mesoamerica and the Andes, regions famously home to large empires, kingdoms, and city-states. In what's now the US and Canada, the estimates range between 8-20 million people.

Second, the 90% casualty rate is derived from deaths by all causes, primarily from early demographic information from the Spanish empire (ie, the more densely populated areas). Multiple waves of epidemic diseases - most, but not all, introduced from Afro-Eurasia - played a big part in those deaths, but they're not the sole cause. There are also wars, famine, forced labor, and other stressors to worry about. The population decline was not immediate or instantaneous. It took decades, in some cases centuries, to reach the population nadir. Situations that would result in mass graves and bonefields are rare.

Since it's Thanksgiving tomorrow, I should definitely mention that the Plymouth colonists discovered just the sort of thing you're looking for when they arrived. As they were surveying the area, William Bratford reported that "sculs and bones were found in many places lying still above ground, where their houses and dwellings had been; a very sad spectackle to behould.” The Plymouth colonists were settling down in an area that had been hardest hit by an unknown epidemic about 2 years earlier. The 1616-1618 epidemic occurred along the Atlantic coast from New England to Virginia, the Wampanoag in eastern Massachusetts took the hardest hit. The Narragansetts in Rhode Island also suffered from it, but not to the same extent, and the Pequots in Connecticut were relatively untouched by it, with only a few scattered reports of the disease occurring south and west of there. This disparity in fatalities is what prompted the Wampanoag to finally let the English establish a permanent colony in the area, since they were eager to have some new allies and access to reliable trade to help re-balance the power dynamics with their neighbors.

Where are the permanent cities and towns, where are the supercenters of trade and cultural exchange?

Cahokia is the most famous of the large Pre-Columbian population centers north of Mexico, though its not particularly useful here. By the time Columbus arrived, Cahokia was already abandoned as the population had largely dispersed into numerous smaller settlements throughout the surrounding area.

Ironically, the major population centers that Europeans actually interacted with are less well known. These include the recently-rediscovered Etzanoa in Kansas (population estimates range from 12,000 to 20,000) and the still-missing Ivitachuco near Tallahassee, Florida (two Spanish accounts of give a population of 30,000 - 36,000), both of which were around in the early 1600s. In the case of Ivitachuco, there's also an argument to be made that these estimates were intended to represent the Apalachee population as a whole, not just those living in Ivitachuco. We'll need to actually find the place to start figuring that out.

The Cahokians were kind enough to build several gigantic earthen structures that make the site easy to find these days. The other two were sites of mound-building. Throughout eastern North America, most architectural traditions - especially for residential structures - relied exclusively on wood, and unfortunately for archaeologists, wood decays. If we're lucky, we can still detect the post-molds, which usually appear only as a faint discoloration in the soil from where the supporting posts for the structure were. They don't call attention to themselves the way earthworks and stoneworks do. This is part of the reason why historic population estimates for the region are so difficult. Even large population centers can become virtually invisible after all these centuries.

In the southwest, it's a bit easier, since the major sites there tend to be made of stone and leave a more noticeable footprint. But that's not my area, so I'll leave it for others to discuss.

I wasn’t arguing that there weren’t significant population centers in North America (after all, the Spaniards had never seen a city as impressive as Tenochtitlan), but that there could not possibly have been 100 million people in North American before 1491. There were 106 million people in North America, from Alaska to Panama, in 1900. There were dozens of cities larger than Tenochtitlan at its greatest, and several 10 times as big. I don’t think there is evidence supporting the idea that the continent was more densely populated in 1490 than in 1900. And the Black Death maybe killed 50% of a vastly more densely populated Europe, so a 90% death rate in the Americas doesn’t seem right. I’d suppose the Native population in North America was 20 million or less, with a somewhat larger number in South America

OP I kind of feel like your question comes across as an issue with the study of history in general and not necessarily an issue within the scope of this topic. The reason I say that is because obviously we don't know for sure, how could we. However, best academic work available has some pretty good ideas. These ideas would put death rates in mesoamerica over 90% due to the combination of desease and famine as well as other factors. The largest difference with native populations is that they did not live as closely with animals as Europeans did and thus had almost no inherent resistance to many deseases. Further, high death rates could cause a break down in society and lead to things like famine or wars of revolt. We are even now (2008) still locating the remains of huge population centers in Honduras that were completely lost to the jungle. If your honestly curious how the 90% death rate is possible read the sources below.

Acuna-Soto R, et al. Med Hypotheses. 2005.

Acuna-Soto R, et al. Emerg Infect Dis. 2002.

Estimating population is always tricky when we don't have accurate demographic data (and even then there are issues for the data) even for a place like medieval Sweden the estimates can vary wildly (and as far as I can tell the academic consensus is "We don't really know", with an upper and a lower bound, but with a great deal of uncertainity in between)

The larger and more diverse the area (and North America is very large and diverse) the more complicated the estimates get, and it often becomes a matter of trying to define estimates. The tendency in recent years (as evidence has proliferated on settlement patterns, etc.) to increase the count for North America, but it remains a great deal of uncertainity.

The differentiation in numbers tends to largely come from "How much do we extrapolate evidence from the areas we have something of an idea of?" We can somewhat estimate the population of Tenochtitlan, but how representative is that area? (Most would probably say that it is an outlier, but to what extent?) Is the Southeastern US (which was fairly densely populated) representative for say the Northwest? Even relatively small variations can lead to vastly different outcomes. (and even then this focuses largely on urban sites, but we know that some areas at least can sustain a fairly dense population without neccessarily having that large city centres, which further makes things more uncertain)

But as others have pointed out, the main problem is the conflation of terms: "North America", technically includes Mesoamerica, but doesen't neccessarily do so in everyday speech (where the Latin/anglo distinction is often used) I've run afoul of that myself (its also confused by the fact that while there is an official UN definition, different languages sometimes define the continents slightly differently)