My dad was also a US Merchant Marine in WW2, aboard oil tankers in South America and Africa. I sent a request for his military records to the following address:
Commanding Officer
USCG-National Maritime Center (NMC-421)
ATTN: Correspondence Section
100 Forbes Dr.
Martinsburg, WV 25404
I also submitted a request through vetrecs.archives.gov and I received information from both agencies. (This was about three years ago; I don't know if budget cuts still make it possible.)
Here are a couple of other very helpful sites:
Merchant Marine Service Records including Voyage Discharges from U.S. Coast Guard:
http://www.usmm.org/contact.html#contact3(The whole USMM site is great!)
Convoy Web (The Website for Merchant Ships during WW2)
http://www.convoyweb.org.uk/Happy searching!
Nancy