The prices can really vary with demand, especially near Union Square. Also, be aware that any hotel in SF will charge 30+ for parking, and It'll be closer to $50 near Union Square.
I've had good experiences at two of the Joie de Vivre hotels. The Hotel Tomo is about a mile and a half away from Union Square in Japan Town, and is a nice midlevel hotel. The Galleria Park is really well located, though it's of course more expensive.
What brings you to the area? Will you have time for any empeg related activities?
Matthew