Hotels see
http://www.disboards.com/showthread.php?t=2701656&page=2 post #27 for the photo that shows Pier 91 in relation to downtown Seattle. Please plan on needing transportaion to the pier unless your hotel provides it.
Things to consider as you book:
Other than the Doubletree Seattle by the airport, I have not personally stayed in any of the hotels. I just drive in or take the sounder when I head downtown. I am giving information on where hotels are located, location and walking. Please google the hotel for reviews for specifics of how people liked it and for pricing. (or ask here and we will try and anser questions. I will try and update all the information given into this post)
I would like to add that you only go to and from the pier once. You will be coming and going from your hotel to attractions more, so having a convenient hotel to the attractions you want to see will save in the long run.
However, Seattle is a green city and has a great transportation system. It is possible to only need a taxi to the pier and take public transportation for the rest of the time.
If you have a car, check for parking fees at your hotel.
Also daily parking fees in Seattle are killers if you need to move your car mid day. If you can take public transportation you can both avoid fees and the crazy one way streets.
A hotel with a one bus/trolley option to either Westlake Center or Seattle Center will make your mobility much better. Most things people want to see are by these two places. Most
Citypass events are at the Seattle Center, while Westlake is more centrally located overall.
(If you have an early flight home, I would try to be by Westlake Center for ease of light rail to the airport or train station. The monorail does not open until 7:30 M-F and 8:30 on weekends)
Getting to/from the Seattle Center(Space Needle etc) to Westlake Center on the monorail is easy. A hotel by either increases your ease of transportation.
From Westlake monorail it is a downhill walk to Pike Street Market. You can walk to Pike Place Market, and take the elevator from there down to the waterfront. (Ask for the elevator location as it is tricky to find if you do not know where it is- or in our case that it even existed)
Also from Westlake it is a short bus ride to Pioneer Square.
Disney arranged hotels are:
Sheraton Seattle- by Westlake Center,"Very nice" 3 block walk to Pike Street Market It is a block and a half from lightrail. You can exit the Westlake Station at Nordstrom which is on Pine St. between 5th and 6th Ave. The Sheraton is on the corner of 6th and Pike. If you have tons of luggage, take a cab. If you travel light the light rail works great. Have not confirmed Disney is using it.
Westlake Center is centrally located includes a mall with a food court:
Mayflower Park if you want to go upscale, the Mayflower Park is a good choice. It's about a mile or two (maybe less) from the port, and you can take the light rail there from the airport. You can also take the monorail to the Seattle Center. You can walk to Pike Place Market, and take the elevator from there down to the waterfront.
Westin two really tall round buildings that leave you with pie shaped rooms! Walk to Westlake to catch the monorail to Seattle Center, walk to Pike Place.
Homewood Suites Convention Center Sits over I-5 hotel comes with ear plugs. A bit farther of a walk. Pedestrian concerns seem not to be an issue. Recommend you google this one and read the reviews to decide. More info later.
Seattle Center Area hotels:
Best Western Executive Inn You can walk to the Space Needle, monorail, Experience Music Project, the Sci-Fi museum, and the Pacific Science Center. You can also take the monorail to Westlake Center, walk over to Pike Place Market and take the elevator down to the waterfront. Take a car or taxi to the port.
Lake Union hotels:
Residence Inn Downtown/Lake Union on Fairview Ave North gets good reviews as long as you are not parking (Narrow parking spaces). There is a SLUT stop right in front of the hotel. (SLUT=South Lake Union Trolley) This also puts you close to a really nice grassy area park. I figure that is really important for anyone that has kids. More Lake Union than downtown. The Residence Inn is not really within walking distance of anything downtown. (Pike Place Market, EMP, Space Needle, etc) It's probably close to a mile to walk to Seattle Center where the Space Needle, EMP, Science Center, etc are. It's not a walk I'd want to make. It's partially uphill, part of it walking on a narrow sidewalk through an underpass. To the best of my knowledge, there aren't any real "family-friendly" restaurants in close proximity to the hotel. You'd have to go back closer to downtown for that. As NWmom said there is the trolly close to the hotel that would take you more into downtown. I don't consider the location of the Residence Inn "downtown'.
Airport hotels:
Holiday Inn Express-If you want to go downscale They have a decent breakfast, good prices, and you can take the shuttle to the airport and catch the light rail into town pretty easily, although you might have a time of it getting to the port on public transit.
Doubletree Seattle and Convention Center Pretty much across the street from the airport.
Waterfront hotels:

(Disney is leaving from Pier 91 so waterfront hotels are not as convenient as they sound. They may or may not be convenient, check their location to the pier Disney is using)
Marriott Waterfront - it is <5 minute walk to Pike's Place market.
Pioneer Square hotels: certain areas you might not want to be at night, farthest from Seattle Center. The ones listed are in safer areas see the previous post discussions. This area is close to the Amtrak station for those coming by train. The train station has taxis.
Courtyard- very good
International district hotels: Not recommended at night