Hellobee Boards

Last time we were in SF, we stayed at the Omni, and we loved it! It is a little pricey, but the rooms are nice and big, and the bathroom was huge (with french doors) so we put DD in there at night. The staff was super friendly and really nice about DD (they gave her toys, played with her at breakfast, etc...). And, when you're staying with a baby/child they bring warm cookies and milk to your room every afternoon. Overall, we were very impressed with the service we received at the SF Omni; we've since stayed at other Omni hotels, and SF is still our favorite!

They are in the financial district, so it is pretty quiet on the weekends, and they often have discount packages for travelers Friday-Sunday: http://www.omnihotels.com/FindAHotel/SanFrancisco/SpecialOffers.aspx
We've also stayed at the Holiday Inn at Fisherman's Wharf before (before we had kids), and that was fine, too.

We went there last summer and I cannot think of the name of the hotel we stayed at! The room was nice and spacious, but the noise from the street was terrible. There were people yelling on the street all night long and we could hear them on the 20 something floor. The hotel even supplied new earplugs daily. Definitely bring a sleep sheep or noise machine for baby!