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I live in Seattle. I think the least expensive and good location place is Pension Nichols downtown. The website is: http://www.pensionenichols.com/book.html. If they don't have space - they might be able to recommend another place. I think it's around $135 a night for 2 people.
The hotels along the waterfront are very expensive. You can get a little better price staying near the Seattle Center at the Courtyard at Marriott or Comfort Suites Downtown Seattle but they will be around $100 pp per night unless you get a deal from expedia or something. If you go a little further out - you can try the Silver Cloud Inn at Lake Union.
Try tripadvisor dot com for recomendation.