If you go to Berlin, I would definitely take the cruise ship excursion. There are WAY too many things that can go wrong being that far from the cruise port that can make you miss the ship. Feasibly if you have from, say 7 am to 7 pm, and 6 of those 12 hours are for travel (assuming there are no delays, stops, etc.), and you need at least 30 minutes wiggle room on either end for contingencies, and at least 30 minutes for lunch, really you only have 4.5 hours to work with sightseeing-wise. I would pick 1-2 sites that are close together if doing it independently or with a dedicated guide, but on a bus tour from the cruise ship, they will take care of the logistics of moving you from place to place, guiding you around, etc. We did this in Rome and felt very good about our "Rome in a day" bus tour--got to see a lot. But of course Civitavecchia is only 1.5 hours from Rome as opposed to 3 hours from Berlin.
As far as the sites you see, it depends on your interests. We are going to Berlin this summer and plan on seeing the Berlin Wall Memorial, doing an underground bunker tour, visiting KaDeWe department store, doing the DDR museum, and seeing the Brandenburg Gate and the Reichstag. None of those things, except the gate and Reichstag, are remotely close together. So definitely look at Google Maps and plot out what interests you, then choose things that are continuously close.