This is a tremendous open question. We have one report from an early Spanish traveler, Gaspar de Carvajal, who was part of an expedition (of raiding and conquest, let's not mince words) CA 1540. His diaries recorded what appears to be a large and thriving, although fairly distributed, civilization throughout the Amazon basin.

There are also important secondary indicators of large-scale civilization in the pre-Columbian Amazon: perhaps most interesting is the major Andean temple site at Chavin de Huantar, which was a major pilgrimage site from CA 1200BCE-400BCE. What's interesting about it (from this perspective) is that it's absurdly inconveniently located from the perspective of all the Andean civilizations of the time of its founding, but would be a highly convenient midway point between the Andes and the Amazon. The prevalence of imagery like jaguars in Andean religion (both at Chavin and elsewhere) is also suggestive, because jaguars don't exist over there - only in the Amazon. These suggest significant interactions between coastal and high Andean societies with people in the Amazon basin.

Why am I talking about all this incredibly circumstantial evidence? Because that's nearly all we have. The same expedition that brought Gaspar de Carvajal to the Amazon also brought the Great Pandemic, the outbreak of European plagues which nearly wiped out all of humanity in the Americas. By the time the next Spanish travelers showed up, the Amazon was as sparsely inhabited as it is today.

If this happened in Europe, Asia, or Africa, archeology would help, but in the Amazon construction has always been overwhelmingly out of wood (for obvious reasons), and if you've ever been there, you'll know that anything, especially plant matter, left unmaintained in the Amazon is going to become part of the soil really fast.

There is current research using satellite imagery to try to identity the remains of larger structures, or more likely patterns of agriculture, from orbit, but AFAIK there isn't yet anything conclusive.

If I had to bet, I would say that the Amazon was very densely settled, and was probably the home of some of the richest and most interesting civilizations of the pre-Colombian Americas - but it's going to be damned hard to know for sure.

NB that you asked about Brazil, which of course is much more than the Amazon, but I don't know anything useful about the more southern parts of the country in that period.