At the end of a GCT tour last year, we stayed at the Hotel Fita, which was favorably reviewed on Tripadvisor. It's small but comfortable, and the staff are very helpful. Since it is popular and fairly reasonable in price, you need to book pretty far in advance. It is well located for museums and sightseeing, but not extremely close to the ship dock. However, the ship dock is right by the railroad station, and there are convenient trams from the Fita to the station. We managed pretty well on the tram in non-rush-hour traffic with a roller suitcase and a carry-on each.
One bit of advice for sightseeing: it saves a lot of standing in line to buy tickets on line in advance for the Anne Frank House. The tickets are timed, but you can arrive a bit early and they still let you in (don't know what would happen if you arrive late).