We stayed a couple nights a couple years ago at the Holiday Inn Express & Suites. It was nice and within walking distance to Pier 39, Ghiradelli Square, Lombard Street and Pier 33 (ferry to Alcatrez). I just checked and we paid almost $275/night (including taxes and fees).
Just be sure to check bedbugregistry.com and check yelp (search for bed bugs) before you book. I say this as a longtime SF resident. Trust me.
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