Haze Gray & Underway
http://www.hazegray.org/

Mariners
http://www.mariners-l.co.uk/

Maritime Administration (MARAD)
U.S. Department of Transportation
http://www.marad.dot.gov/

MARAD Update.  Official Journal of the Maritime Administration
http://www.marad.dot.gov/HEADLINES/newsletters/newsletters.html

PMARS Property Management and Archive Record System
http://www.pmars.imsg.com/default.asp

Military Sealift Command (MSC) (ex-Military Sea Transportation Service MSTS)
MSC-Military Sealift Command

National Oceanic & Atmospheric Administration (NOAA)
U.S. Department of Commerce
http://www.noaa.gov/index.html

NOAA Magazine
http://www.magazine.noaa.gov/

NOAA Ocean Explorer
http://www.oceanexplorer.noaa.gov/

NOAA History
http://www.history.noaa.gov/index.html

NOAA Central Library
http://www.lib.noaa.gov/

Naval Historical Center
http://www.history.navy.mil/index.html

Ships History Branch
http://www.history.navy.mil/branches/nhcorg9.htm

Naval Oceanographic Office (NAVOCEANO)
https://www.navo.navy.mil/

Major Shared Resource Center MSRC
http://www.navo.hpc.mil/

Maury Oceanographic Library
Naval Oceanographic Office
http://library.navo.navy.mil/

Naval Research Laboratory
http://www.nrl.navy.mil/

Naval Research Laboratory, Stennis Space Center
http://www.nrlssc.navy.mil/

Naval Vessel Register
http://www.nvr.navy.mil/

NavSource Naval History
Photographic History Of The U.S. Navy
http://www.navsource.org/

Office of Naval Research
http://www.onr.navy.mil/

Office of the Oceanographer and Navigator of the Navy
http://www.oceanographer.navy.mil/

Scripps Institution of Oceanography
http://sio.ucsd.edu/

United States Navy (USN)
http://www.navy.mil/

Universal Ship Cancellation Society
http://www.uscs.org/
NOTE:  Perhaps an unfortunate choice of names!  The Society does not actually cancel ships (I'm sure you're relieved), but promotes the study of the history of naval vessels, naval postal markings, and other postal documents involving the U.S. Navy.

U.S. Naval Institute
http://www.usni.org/

Victory Ships
http://www.usmm.org/victoryships.html
http://en.wikipedia.org/wiki/Victory_ship

Woods Hole Oceanographic Institute
http://www.whoi.edu/

World Ship Society
http://www.worldshipsociety.org/