I have to think there's some kind of reference to a deceased character when AJ mentions he's speaking to the ghost of a "sea captain". As far as the sea/water theme, it could be Big Pussy Bonpensiero. If I may delve into the supernatural for a second, it seems like Big Pussy would be the logical ghost to haunt AJ. Pussy was AJ's godfather, and bared his soul to him way back in "D-Girl". Alternatively, it could be Ralph Cifaretto, whose status as a captain was frequently brought up, and who appeared in Tony's dreams this episode.
Taps, lights out, 2200 hours. What's missing? Give up? Television.