first of all welcome to Cruise-Chat.com.
A most interesting question, indeed. I know all of the ports in question fairly well, and it is difficult to give an answer.
IMHO Bremerhaven has the best facilities for cruise ships, followed by Kiel, while Hamburg in particular is by far my least favorite port when it comes to this. Warnemünde recently had a new terminal building constructed, which from the pictures I have seen is similar to what is offered in Kiel. The Bremerhaven terminal still appears to be better, though.
As far as the infrastructure is concerned, Bremerhaven has disadvantages, also when it comes to interesting sights nearby. Hamburg, Kiel and Rostock are much more interesting cities.