With your focus on radical Southern history, I would recommend contacting Gregg Michel at UT-San Antonio: http://colfa.utsa.edu/HIST/Faculty/michel.html He published a book last year, Struggle for a Better South: The Southern Student Organizing Committee, 1964-1969, and he probably knows the radical Southern history scene.
I doubt there exists an entire program with a focus on radical history. More likely you'll find one or more radical historians in certain programs. I recommend following leads (books, articles in Radical History Review which is published by Duke University) around your topics of interest and finding out where these people teach. I also recommend joining discussion lists such as H-RADHIST and asking your question there.
Hope this helps!