There defintely used to be many more flag ships floating around the seas. The ones I do know of...
Navy Collosus (War Galleon) around level 35 to 37 behind Cuba.
EITC Barracuda (War Sloop) usually level 26 to 28 floating near Driftwood Island.
Navy Kingfisher (War Sloop) around level 21 near Port Royal
and a couple Light Frigates (mostly EITC I see...) floating around...
Just from my observation...
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Shhlatkinz 
The Guardians
(remake of The Brotherhood)
Notoriety 40
Pirate Master
Toontown
Cool Corny Electrofoot, Nacho Average Pig, Cool Corny Electrofoot Blak