I found a couple custom tilesets designed by fans, but they leave a lot to be desired. Trouble is, RPG Maker VX Ace does not include a tileset to be used for designing ship maps.

Well, in my work on the harbor town I'm designing, and the nearby sea shrine, it came to me that I'm going to need to have a scene on board the ship that your group eventually acquires the reins to. Although in the first Final Fantasy, there was no separate map to indicate being on board the ship (or airship), I seem to recall one in Final Fantasy IV (probably just before the entire gang got attacked by Leviathan), and there were certainly scenes of that nature in Final Fantasy VI - even more so if you include the airship. The on-ship cutscene is a staple of classic RPGs.