If Europe had the technology of the Native Americans, and the Native Americans had the technology of the Europeans, the exact same thing would have happened. The Mezoamericans had huge empires, a few of which were notorious for their military conquests.
Basically, discovery is a two-way process. The Native Americans would discover the Europeans at the same time that the Europeans discover the Native Americans. The questions become:
1) Where is the fight occurring, in the Americas or in Europe?
2) Who has the technological advantage, Americans or Europeans?
The premise of this question appears to be that the answer to question one is that the fight is occurring in Europe.
Assuming that the Europeans had the technological advantage, they would easily fend off any Native American invasion. They might even treat Native Americans as some sort of curiosity, nothing to be feared. Eventually, one European ruler will decide to find the Native American’s home country, and then they will proceed to take it over.
This isn’t super-realistic. Since the Native Americans would be the discoverers and were able to cross the Atlantic before the Europeans, it is quite likely that they would have had the technological advantage. In this case, they would have done the same thing to the Europeans that history tells us that the Europeans actually did to the Native Americans. They would simply colonize the land and push the Europeans off of the land.
Anyways, this whole question is “What if the Native Americans discovered Europe first, and not the other way around?” A much more interesting question, in my opinion, is ”Why didn’t the Native Americans discover Europe first, instead of the other way around?”