A planned cruise is docking at a port of call on shabbos and I advised my friend that leaving the ship is not allowed for issues of domains (rishuyos). In a different question posed, you mentioned that leaving a ship on shabbos as long as the destination and malacha is prearranged may be acceptable. Is disembarking and embarking a ship at port that arrived on shabbos and will be leaving on shabbos with you on the ship at its arrival and departure allowed?

There are many factors involved in allowing embarking a ship before Shabbat. They are discussed at length in Techumin Vol. 10, by Rav Moshe Hadaya the Chief Rabbi of Eilat. One of the main factors allowing embarking a ship before Shabbat within 3 days before Shabbat is that the voyage is for the sake of a mitzvah or for business.(Rema O"H 248: 4). The Rishon Letzion the Gaon Rav Mordechai Eliyahu (who at the time of the writing of this answer is hospitalized, may Hashem grant him a refu'ah shleima) set down a few rulings in the aforementioned book. 1. If the ship is docked at a port all of Shabbat and the ship will sail Motzei Shabbat, passengers may disembark and reenter on Shabbat, provided that they have nothing on their person to avoid the prohibition of carrying and they do not go further than a distance of 2000 Ammah =960 meters from the ship to avoid the prohibition of Techumin. 2. If there is a doubt as to the possibility of desecration of Shabbat since the ship may sail, the passengers should remain aboard the entire Shabbat. 3.One should avoid sailing on a ship if there is planned sailing on Shabbat from one of the ports of call. However, if it suddenly became known that there is a planned sailing on Shabbat, passengers mustn't leave the ship at all, but should remain aboard.