When I think of people like the Maya, or the Aztec, or the Inca, I have to admit that my only lightly-informed view of them doesn't really have anything in it about how non-hetero people lived and were treated. I presume they existed among those populations, but what were their lives like? Do we know?
The issue here becomes differentiating between pre-contact views and post-contact views, which is exceptionally difficult. Without a lot of pre-contact sources, generally what we have are either European accounts or accounts influenced by European biases. This generally gives the impression that while non-hetero sexualities existed, they were frowned upon or demonized as they were in European societies.
This becomes even more difficult because later indigenous writers also became influenced by European morality, and this effected their view as well, even as they tried to keep a traditional world view.
It’s also has to be recognized that there wasn’t just one view either, which is often a trap some fall into.
So, with that said, we can be certain their were non-hetero individuals. We do have records of that. Europeans did write about such, but generally it came off as either apologetics or accusatory, which makes it nearly impossible to distinguish what reality was.
The people of Mexica, the Aztec Empire, appeared to be intolerant. Others, like the Mayans, seemed to have a connection between non-heterosexuality and ritual. So they were associated, often, with shamans.