Before getting into the meat of this, a note has to be made. To speak of Pre-Columbian Americas is extremely difficult because we lack when it comes to historical records. Many of these cultures were oral cultures, and the stories weren’t written down until after European contact. They were often written down by Europeans, and European ideas were sometimes interjected into the stories. So such study is always a bit difficult.
Second, we also have to be aware that Native Americans are a wide and varied group that had many different cultures, practices, and such. We can’t treat them as a monolithic culture.
So to the question. I think the easiest way to look at this would be to look at prostitution among Native American tribes as well as rape (especially as a product of war).
Juha Hiltunen, in “Spiritual and religious aspects of torture and scalping among the Indian cultures in Eastern North America, from ancient to colonial times” does a terrific job of examining the rape aspect. They mention two important aspects. First, rape of women was more rare when it came to war. Most likely this had to do with the fact they could bear children. However, men were often raped when it came to war, and the act was to make them like a woman. The raping of men was often very brutal. So sexual assault did occur, but it was more focused on men then women, at least in the context of war. To be clear those, this was under matrilineal tribes. In these tribes, women and children were the ones doing the raping and conducting torture in general.
Going to prostitution, many Native American tribes forbid it. But it was still practiced. We can look at the Aztecs for whom we have some records. It was officially forbidden by the Aztecs, but prostitution is still mentioned in various sources. So it existed, but wasn’t openly accepted. We see this among the Tarascans as well, who were contemporaries of the Aztecs. It was offically against the law, but for them, it was openly tolerated. The 16th Spanish chronicler, Anton Caicedo says this about prostitution among the Tarascans:
This witness has been in many marketplaces [tianguez] of that province [Michoacan], and before this sin of sodomy was punished, this witness knew of many times that, when he asked the Indians why they made sacrifices and idolatries and sodomies, they told him that in the markets there were sodomitic Indians who were accustomed to do this and who carried it on as a business and for profit and who had it as their trade to be sodomites and to be in the afore-said marketplaces and to do that sin and abomination with the Indians who paid them for it; and frequently a Spanish interpreter pointed out to this witness in the marketplaces some of the Indians who it was said carried on and practiced this sodomy.
Prostitution doesn’t equate to sexual assault in all cases, but it does when that woman is being sold by someone else, and that was apparent in such cultures.
So sexual assault was existent in Pre-Columbian Americas. The idea that it didn’t happen really rises out of the Pan-American movement of the 60s and 70s, and the myth of the Nobel Savage. As we saw above, we do have examples of it happening, and at least in regards to warfare, it was widespread.