Seattle is not very big, so as long as you stay in downtown, you should be able to see everything and still be close to the pier.
Do you have a budget in mind? The Edgewater Hotel is super famous and right next door. Hotel 1000 is very, um...trendy? Eclectic? But fun and they have a great restaurant.
Then again, I do not find Seattle to be very big, and it's quite walkable, so most hotels that are in the downtown area would be fine.