Yes. If you are required to obtain K-ETA and plan to enter Korea without a visa, you must receive approval before boarding not only a flight but also a ship, including a cruise ship or ferry.
This also applies when entering Korea through ports such as Busan Port or Incheon Port. What matters is whether the traveler is subject to the requirement, rather than which Korean port is used for entry.
You should obtain the required travel authorization before boarding the ship bound for Korea.
If you plan to travel to Korea by ship, apply for K-ETA well before your departure.