I don't get why a Mongol invasion, successful or not, would prevent the eventual discovery of the Americas by Africans or Eurasians. The centuries in which the Europeans are not involved is irrelevant to immunity. As pointed out earlier, one cannot become immune to diseases that neither you nor your ancestors faced. The most advanced Amerinds were in the equivalent of the bronze age and lacked many of the advantages that led to European population density (the most notable and important of these being the lack of large livestock). Someone would discover it eventually, either on purpose or by accident. The West African peoples, both Arab/Berber and Black, were sailing further and further west on expeditions. The Basques, Bretons and Scottish fishermen were expanding west. Many myths of lands to the west, as well as the colony in Greenland, could fuel the imagination of explorers.
Nevertheless, I guess an increase in Amerind population, as well as the formation of states north of the Mesoamerican cultural area. The Ecuadorian trade network and the Mesoamerican one would gradually grow closer (they already had some contact, based on the existence of some South American insects in Mexico, and the Mesoamerican trade network was already trading with the Caribbean one, which traded with Floridans and the Guyanas), allowing for the vital exchange of gods and information that speeds up the rate of innovation. A larger population in total would mean a larger total amount of survivors of disease. The main savoir of the Amerinds in this scenario might be a difference in the approach to colonization rather than greater Amerind advantages.
ìtsanso, God In The Mountain, may our names inspire the deepest feelings of fear in urkos and all his ilk, for we have saved another man from his lies! I welcome back to the feast hall kal, who will never gamble again! May the eleven gods bless him!