Excursion done with Alla Tours - excellent in every way, Do not be deterred by the 3 hour bus trip each way. They stop once in each direction and the bus is quite comfortable. Just watch the scenery or go to sleep. Berlin is worth it if you have not been there before. Highlights were the Brandenburg Gate, the Berlin Wall and Checkpoint Charlie. Visited many other sites as well
This was the high point of the cruise. Two day excursion done with Alla tours - excellent. We saw so much and with a group of 14 (they never exceed 16 with their groups) we were able to get in and out of the very crowded museums and churches much more expeditiously than the larger tour groups and I think we saw more.
Don't even think of doing this city on your own. You need a visa for one thing, and there is a big language barrier. With Alla tours (in fact with any tour company) they look after the visa. So do a ship's excursion or better yet, go with Alla Tours or one of the other very professional local tour companies you can read about on Cruise Critic.