There are many hotel choices in San Francisco. However, there are two big conventions in the city the week of HGV2015 so many hotels are charging really high rates. We suggest that you go with the boutique hotels in the Union Square area, where it is safe and convenient to get around. Some 3-star hotels are charging <USD 250/night plus taxes and they are good values. You can get to a MUNI subway station (at Powell and Market or Montgomery and Market) on foot (~5-10 min) and get to the Mission Bay Conference Center on the KT train (18 min train ride followed by a 5 min walk).
Another option is to stay near the San Francisco International Airport but within walking distance to a Caltrain Station (http://www.caltrain.com/stations/systemmap.html) or a BART station (https://www.bart.gov/schedules/bystation). The hotels in Milbrae and San Bruno are substantially cheaper than the city hotels and you can take Caltrain (to the San Francisco Station at 4th Street and King Street) or BART (to the 16th Street Station in San Francisco). At both stations, there are free UCSF shuttles that will take you to the Mission Bay Campus (see Venue and Travel).
The last option is to use Airbnb (https://www.airbnb.com), where you can rent a room or just a couch from local residents. Look for places that are close to a UCSF shuttle stop (http://campuslifeservices.ucsf.edu/upload/transportation/files/System_map_072014.pdf) or a SF MUNI stop.