We stayed at the Hotel Edgewater which is right next to the Bell St. cruise terminal. We didn't leave from Seattle but couldn't pass up the chance to see the city. The Edgewater is right downtown on the waterfront and within walking distance to all the attractions....three blocks from the Pike's Place Market, Pioneer Square and the shopping districts.
I would opt for a bayside view looking out over Elliott Bay. Rooms were not huge but the staff is very friendly, nice restaurant and bar.