The administrative chain of command:
President of the United States: President George W. Bush
Secretary of Defense: Honorable Robert Gates
Acting Secretary of Navy: Honorable Donald C. Winter
Chief of Naval Operations: Admiral Michael G Mullen, USN
United States Naval Academy Superintendent: RADM Jeffrey L. Fowler, USN
Commandant of Midshipmen: Captain Margaret D. Klein, USN
I think this is up to date.