By any measure of technological and material progress, the Europeans were clearly superior to the Native Americans. It is harder to say who was superior in terms of cultural and societal values.
When we talk about the superiority of one people over another, we are generally talking about material superiority. On this measure, there is no question about who was superior to whom. The Native Americans had relatively little technology. They did not have metal tools or weapons. They did not have woven cloth. They did not have things like ships that would enable them to travel across the sea the way the Europeans could. This clearly shows that the Europeans were materially superior.
There are those who might argue that the Native Americans were superior in terms of their values and the ways in which they saw the world. People might argue that the Native Americans were less materialistic and less prone to harming the environment. They might argue that the Native Americans were more egalitarian. There are two problems with making any such judgments. First, we cannot really know what the Native American societies were truly like because we do not have good, objective, scholarly descriptions of them. Second, and perhaps more importantly, it is impossible to objectively say which values are superior to which other values.
Thus, in material, measurable ways, Europeans were superior. As far as values go, it is not possible to say.