We stayed at the Holiday Inn Express in February 2007 and it was fantastic. I can recommend it to anyone wanting a fishermans wharf area hotel as not only are the rooms spacious and clean, but you also get a free continental breakfast which is a rarity in the U.S.
There is also a Sports bar opposite which has a friendly atmosphere (much nicer than the bar at the neighbouring Holiday Inn!) Only problem with this area of the town is the distinct lack of nightlife but regular trams take you up to Union Square where it is much livlier.
A great hotel at a great price