I served on the U.S.S. Independence.  We called her, Indy, Chicken of the Sea, Flat-top, Ship, and maybe a few other names, but we didn't call her a "boat".  I just scanned through my 1961-61 cruise book (The Profile) and all references I found were "ship". 
Calling her a "boat" would have been as inappropriate as calling a "piece" a gun.  Piece is the naval term for a rifle, for example.  A"Gun" is that big old cannon that goes boom on a destroyer  or similarly armed vessel. lol