Well, to be fair, the Aztecs (Mexica-Nahua) did not know about the Inca. They may have had rumors, but nothing solid. The Incas, by the same token, did not know about their northern American cousins either. The Yucatec Maya were known by the Nahua since the Yucatec and Maya peoples may have been trading with Mexican coastal societies and even Teotihuacan well before 450 CE. Some would even argue that Teotihuacan-related groups may have started settling the Yucatan during the first half of the first millenium and that Classic Maya refugees fled into those areas and adopted/blended new cultural traits into their own. Demarest provides an interesting interpretation of that in Ancient Maya. So, while the Nahua knew about Yucatec Maya (but probably not about Classic Maya sites and history), they did not know about the Inca nor did the Inca know about the Mesoamerican civilizations.

That being said, it is unlikely that the Tupi knew anything about the Inca, either. Remember: the Inca only began to develop their imperial system in the early 1400s. During that time, from Pachacuti's expansionist policies to the Battle of Cajamarca just over a century later, the Inca managed to claim the Pacific side of the Andes by and large. The Amazonian Andes were relatively ignored and the southern limits of the Empire moved into modern day Argentina, but nowhere close to the areas that the Tupi-Guaraní inhabited. Even the Gê cultures of the rainforest did not have significant contact with the Inca. The Tupi probably had some trading contact with the groups south of them, like the Mapuche and other groups that lived in the pampas, but I have never read clear evidence to back that up. As much as we might like to think that these peoples were as well travelled as the Europeans and Africans that first encountered them, they were not. Most lived in small, tight-knit communities that kept to themselves. The few groups that did encounter the Inca in non-Andean zones were some of the nomadic hunters in what is northern Argentina, but they were not organized into what we might call an ethnic resistance against the Inca.

The fact remains that the Portuguese encountered a less densely populated part of the Americas inhabited by peoples with different cultural traits than those of Mesoamerica and the Andes. The groups that Columbus, Soto, Coronado, Menendez, and Quesada discovered might be better examples to see how Europeans treated groups that better resembled Brazilian native groups encountered by Portuguese merchants and explorers.