Have read prod and cons on day tour from cruise ships in Warnemunde to Berlin. Are independent tours by train available?
You can travel yourself by public trains (https://int.bahn.de/en) to Berlin and do a (guided) tour there.
It depends on what you are looking for. It is doable both with a tour and by yourself with trains - but either way, it will be about 2-3 hours one way, so you will spend most of the day traveling. So unless there are only one or two things in Berlin that have caught your interest and you don’t think you will be in Berlin again, I would not do it personally.