My personal sense is that San Francisco has gotten more expensive than New York or London. It obviously depends on what's happening at the time and where you're staying but I find with a little searching I can usually dig up reasonable-ish rates in New York and London. In San Francisco, if there's a big Moscone event (which tends to be when I travel there), it's hard to find much even on the other side of town.
Both also have good public transport, which makes hotels further from the event more appealing. (I don't know SF enough to content on transport there).
In general, public transportation in San Francisco isn't very good although it's really not very good to get to the Javits in New York either. However, the Fisherman's Wharf area and Nob Hill aside aside I'm not sure there's a huge amount of hotel capacity in San Francisco outside of a 10-15 minute walk to the convention center anyway.