The Ballad Index has sixteen songs with the keyword combination "ghost" and either "ship" or "sailor" or "navy." In descending order of number of citations:

The Cruel Ship's Carpenter (The Gosport Tragedy; Pretty Polly) [Laws P36A/B]
Lowlands (My Lowlands Away)
The Ghostly Crew [Laws D16]
Nancy of Yarmouth (Jemmy and Nancy; The Barbadoes Lady) [Laws M38]
The Nightingale [Laws M37]
The Flying Dutchman (Vanderdecken) [Laws K23]
Beam of Oak (Rambling Boy, Oh Willie)
Ben Backstay
Stormy Weather Boys
Admiral Hosier's Ghost
The Fog-bound Vessel
The Wreck of the Glenaloon
Bill Jones ('Twas off the coast of Guinea Land)
Willie Was As Fine a Sailor
The Knight's Ghost [Child 265]
The Cruise of the Bouncing Sally

Some of those are a bit marginal, but most of them are clearly sailor/ghost songs.

[Some song titles in this thread have been converted to links by a Mudelf.]