There is more support to the second theory which says they came from somewhere else. The resemblance of their culture, style of living and traditions connect them to two families from Asia i.e. Mongols and Malays. But, again here the problem is their failed connection with the linguistics of those Asian races. They are not in any way connected to those races in linguistics and hence their origin is still a big question mark.
Although there still are questions about the Origin of Native Americans, all the historical evidence connects them to some races in Asia and some of the types (the whites) to a Welsh colony too which has been long lost in the forests of North America. Columbus, found these people first on the Bahamas islands and called them Indians. Till now nobody is sure about their origin though and a big number of people are in the favor of the second theory but, there is evidence against it