travel from Berlin or Hamburg to the port at Warnermunde for cruise ship

Trains from either airport with connections, similar travel times. Take the one with the best flights for you.

Check train connections at DB journey planner.
https://int.bahn.de/en

Recommendation depends on date of travel - comprehensive maintenance works in Northern rail network. Details on this page available (German language only) after entering date (click on "Heute").

I am assuming that you would either explore whichever city you choose or won't explore either and that this in now way factors into your decision. In both cases you would take the train to Rostock, then transfer to the S-Bahn toward Warnemünde. So the question is which city is easier to Rostock.

Hamburg has a pretty consistent train connection every hour from morning to evening. This trip has two connections, each of which seems to always have 10-18 minutes.

Berlin has slightly more frequent but less predictable connections. Some are direct to Rostock, while others have a connection of 7-15 minutes.

Hamburg has a direct S Bahn from the airport to the central station (again, assuming you are flying in and transferring directly to Warnemünde without exploring) every 10 minutes from the only airport platform. You can't screw it up, really. Berlin has two different options which essentially means every 10-25 minutes at one of two platforms. You can get there easily, but you have to pay a bit more attention.

Hamburg's central station is crowded and a bit gritty, but it isn't too confusing to find your track. Berlin has pretty good signage and is a clean and interesting central station, but it can be overwhelming.

I don't think there is a right or wrong answer. Neither is difficult--they just involve the extra steps of transfers. Technically Hamburg has one extra transfer--but the Berlin transfers might be a bit more stressful, both from the airport and on the train route (if you do take the one with a transfer). All of them take comparable amounts of time. So it's probably a matter of more comfortable and cheaper flights for the most part. Oh, and given the rail works (thanks, MarkK for reminding me), the dates might matter, and yes, that would make me more inclined to choose Berlin, which looks less affected.

.... ps: Warnemunde has a lovely beach...

Thanks, Melissa, for mentioning that. I really like Warnemünde. You can easily spend a relaxing day there. A delicious fish sandwich and a walk to the lighthouse, along the cute Alexandrinenstraße, or along the beach.