According to their website, the "Quality Inn and Suites - Seattle Center" is half a mile from pier 91, so it would be a cheap cab fare to the pier. I don't think they do a shuttle service to the pier, but it wouldn't hurt to ask. I can't figure out how to post a hyperlink on this new forum and type in the text that I want, otherwise I would provide a link to that hotel.
I haven't stayed at that particular hotel, but I have stayed at several Comfort Inns, owned by the same company, Choice Hotels.
2007 - Majesty of the Seas (Bahamas)
2009 - Enchantment of the Seas (Western Caribbean)
2010 - Freedom of the Seas (Western Caribbean)
2013 - Golden Princess (Alaska, roundtrip from Seattle)