The only residency for holistic medicine right now (in which you can now become board-certified) is in Denver. Not sure exactly where--but you can contact the AHMA (American Holistic Medical Association). I believe it is a 4-year family practice residency which leads to dual certification in FP and holistic medicine.
I don't know about IM/alternative medicine. There is a program in Tennessee that has an alternative focus--maybe Knoxville? Also, Dr. Andrew Weill has a fellowship at the University of Arizona (Tucson, I think).
Sorry to be vague--these are just bits and pieces I've picked up from meetings, etc.