Be sure to see the Boarding School Experience. It's an exhibition about how the US government put Native American children into boarding schools in the late 1800s to the present day. I was unaware these schools existed. Seriously, we took children as young as 5 away from their families in order to "civilize" them in federally run schools. Its heartbreaking but worth your time to have a better understanding about our not so perfect American past.
Unfortunately you won't find anything else about the ugly truth about America's past and Native Americans. There's nothing about the Trail of Tears or Wounded Knee. Perhaps the Heard Museum will soon have the courage to tell an unvarnished history of America.