From wikipedia... colleges with controversial mascots:
Alcorn State Braves
Central Michigan Chippewas
Florida Southern Moccasins
Florida State University Seminoles
Hawaiʻi Rainbow Warriors (men) and Rainbow Wahine (women) – "Wahine" is the Hawaiian word for "woman"
Since 2000, each team has been allowed to select its own mascot name; most notably, the football team has been simply known as "The Warriors". See University of Hawaii Athletics for details.
Memorial University of Newfoundland Beothuk - The Beothuk aboriginal peoples went extinct in 1829 and the university named was changed to Sea-Hawks in 1987 as the use of the Beothuk name was deemed offensive.
Mississippi College Choctaws
Ottawa University (KS) Braves
San Diego State Aztecs
UNC Pembroke Braves – representing a college originally created to educate American Indians
University of North Dakota Fighting Sioux
University of Illinois at Urbana-Champaign - have removed all official university sanction of Native American imagery, but unofficially, still widely used by students and fans - there is considerable controversy over whether the term "Illini" as originally used at the university was directly related to Native American culture at all, or whether the imagery was added after the fact; documentation tends to indicate that "Illini" refers to the state of Illinois itself and not its indigenous peoples.
William & Mary Tribe – no longer uses any imagery related to indigenous peoples