Whenever you teleport away from a ship, unless you have other people aboard it, your ship automatically ports itself. However, there has been a recent glitch going around where pirate's ships are getting stranded out at sea for no reason, so I'm afraid you may have this glitch. The only advice I can really give you at this point is either wait it out until the glitch undoes itself, attempt to have your ship sunk (find your ship, get an enemy ship to sail near it, and have it sink it) or contact the Live Chat team.
Best of luck!
