We just returned from a Celebrity cruise to the Baltic's. Warnemunde was one of our ports. We did not do Berlin as we felt it was too far and too much traveling for such a short time in Berlin. Instead we went to Schwerin, an hours train ride from Rostock. Rostock is 15 minutes by train from Warnemunde. The train station is less than 5 minutes from the ship. You can see it from the ship just outside the port area. It's an easy ride to Rostock and beyond.
If you want to go to Berlin, I would consider renting a car and driving instead of the train; quicker and more options if delayed. The autobahn is very good and easy to navigate. The zoo area has plenty of parking as well. Personally, I would save Berlin for another time and do things around Warnemunde or Rostock. Warnemunde is a very nice resort town on the water. Some nice shopping, good restaurants and good German beer. This is a good port to relax and enjoy the weather and resort suroundings.