It has a lot to do with climate and societal level. Mesoamerica, the Andes, and the "Intermediate Zone" between them hosted the densest populations in the New World with urban, complex chiefdom and state-level societies supported by early-domesticated, easily-grown, nutritious, indigenous crops. These huge populations were much harder to displace by European colonists, in contrast to the temperate parts of North America, which were less densely populated by small chiefdoms, subsistence-farming villages, semi-permanent horticultural communities, and hunter-gatherer bands. Though agriculture arose early here as well, the crops were less efficient and the Mesoamerican influences spread much slower.
Today, Mesoamerica and the Andes host the largest populations of unassimilated indigenous people in the New World. In Central America, Colombia, and Venezuela, where large, complex chiefdom-level societies were the norm, much of the population is made up of mestizos, zambos, and tri-racial people with a high percentage of indigenous heritage. In the Greater Antilles of the Caribbean, where the densely-populated, chiefdom-level societies of the Taino were long thought to be exterminated, modern DNA testing is showing a significant, surviving element of indigenous ancestry among the modern population. Even along the North American East Coast, where high-yielding Mesoamerican agriculture arrived relatively late, Old World settlers arrived en masse, and most of the indigenous population was displaced, we see an interesting contrast between those tribes which originated in the Mississippian chiefdom-dominated South and the tribes which came from the lighter-populated Northeastern Woodlands. The Cherokee make up the largest modern tribe in the United States with up to 700,000 claimant members, while the largest Northeastern group is the Iroquois with only 10% of that number.
Among the less densely-populated regions of the Pre-Columbian Americas, those societies which settled in places that were less accommodating to Old World agriculture and development had much greater survival success. Examples include the Inuit in the Arctic, the Athabaskans and Pueblos of the Southwestern United States, the Guarani of Paraguay, the Mapuche of Patagonia, and the mestizos of Aruba. In North America east of the Mississippi River, a common survival tactic was, as Iron Maiden identified, to "run to the hills," as mountain-dwelling groups like the Eastern Cherokee and the Ramapo did. The Lumbee, Seminoles, Mikasuki, and Houma found success in thick wetlands, while other groups survived in the plains and prairies that couldn't be cultivated.
It was also common that the regions most beneficial to European agriculture, like California and southwestern Australia, wouldn't be develop much in the way of indigenous agriculture. California, which has a climate suitable to many high-yielding Mediterranean crops, had enough wild resources to support dense populations without agriculture. The Cape of Good Hope didn't really support the tropical Bantu crops of the nearest indigenous agriculturalists, leading it to be avoided by all but hunter-gatherers until European arrival. Similarly, the Maori who settled the South Island of New Zealand had to give up many of their tropic-suitable crops and adapt a less permanent, less densely-populated lifestyle.
