Imagine if instead of Leif Ericson or Christopher Columbus finding humans, they had found (insert your favorite non-hominid humanoid here) with a similar technological development to the humans they did find. Would there be any real difference in the end result (in terms of colonization and genocide)?
It wholly depends upon the culture and genetics of the non-hominids found in the new world. A significant population of Native Americans was wiped out due to the introduction of diseases for which they had no immunity. A non-hominid species probably would not be susceptible to such diseases.
A large portion was also enslaved, especially by the Conquistadores. This would probably be greater in a non-hominide population as they would be seen as highly intelligent animals (I'm assuming with opposable thumbs to have a similar technology level) and would make very useful slaves. Many of the often gruesome acts at the hands of the Conquistadores were intended as terrorization to ensure subjugation and cooperation of the enslaved peoples, not simply to kill them. You would also need to consider the mentality that many had of "kill the men, take the women" which would not occur with a non-hominid species.
Also, their culture would play a large part in the results. Many of the Native Americans had warring cultures and the introduction of advanced weaponry led to more devastating conflicts between tribes. Several tribes allied themselves with the invaders for a variety of reasons which led to them getting drawn into the battles and political struggles of the invaders leading to more death through conflict. During the American Revolution, if tribes had allied themselves with the colonists instead of the British and secured treaties for their service, they may have been able to secure land for themselves in the East. But it's hard to know who's going to win ahead of time.
So yes, the outcome might be different with a non-hominid species.
The same only more so; the societies that discovered the new world were self-righteous, religiously entitled, xenophobes, the cultures they found were wiped out as fast and as thoroughly as they could manage it and the individuals who survived were converted to fit with their conqueror's cultural moires or they were killed. The surviving examples of native American, in the continental sense, cultural practices exist because the people practicing those rituals were humans who bent to the will of the invaders. A non-human culture would not have been given that option by the Christian European powers to whom the human form is sacred and is destined for yada yada yada.... Non-humans would be blasphemous in their very essence, even another hominid species would have been put to the sword wholesale let alone a non-hominid humanoid.