Jane, I responded to your thread on the Germany Reviews forum, but this is a better place for your question.
Just to reiterate, I'm assuming you are flying into Berlin? I would definitely spend 4 nights there if you can manage it. Keep in mind, as Sam mentioned, that your cruise will probably not be starting in Munich but either Regensburg or Passau. So if that is true, it would make much more sense to spend the last couple of nights in Nuremberg. There is a lot to see and do there, and if you are beginning your cruise in Regensburg, it's a quick and easy train ride to get there from the Nuremberg train station.
In fact, it would probably be even more simple to just take the train from Berlin to Regensburg and get a hotel there for a few nights. You could make day trips from there to Nuremberg if you liked, but then you'd be in a position to easily get the cruise with having to travel the day of.
With regards to Munich, you said you wanted to spend some time there. What will you be doing after the cruise? Is it bringing you back to Regensburg? If so, you could always add a couple of extra days to your trip for Munich and then fly home from there, if possible.
When I in Berlin in 2022, I stayed in Hackescher Markt, at the Adina Apartment Hotel Hackescher Markt. My room was a studio since I was by myself but they also have 1-2 bedroom apartments with fully equipped kitchens, washers and dryers and so on. They do have hotels in other Berlin locations as well, but I preferred this location for its convenience to the sites. The staff was friendly and courteous, and the rooms were very well prepared, large, clean and nice. Breakfast is available although given the kitchen facilities, I just ate in my room in the morning.
Also, the hotel is very convenient to the U-Bahn, S-Bahn, and trams, and is an easy walk to the major museums. The DDR museum is only a few blocks away, along with the TV Tower, and Museum Island is a quick 5 minute walk. You can easily walk to Lindenstraß from there, There are several grocery stores a few blocks away along with a couple of wine shops, many cafes and good restaurants. I would definitely stay in this location again.