I still think, honestly, Mississippi would be the best with Tuscaloosa as the leader, given the many cities and accomplishments of the Mississippi. I'd have their unique ability tie into their mound building, maybe a culture gain version of the Korean bonus where they gain bonus culture from every culture building/wonder they build in the capital and have them build Platform Mounds instead of castles, which can be built with Theology and have a GE slot, and increase city attack to 3 tiles away.
Great idea! For some unknown reasons I have always overlooked the Mississippians. But now I see that they would be the best choice for the second native north american civ slot. Based on their success on city building and strong culture. Apache (Mangas Coloradas and Geronimo would be cool leaders!) and Comanche (horse nation) are also good candidates and I am sure Sitting Bull of the Sioux would look awesome, but from now on the Mississippi gets my vote.