This is sad, but the reality is the homicide rate in San Francisco isn't that bad, in fact it's been steadily declining for 30 years and doesn't sit in the top 50 in the united states.
Both of those sources are from third party sites without valid sourcing. I think it's important to note that while researching a rebuttal for both of these sources you guys provided, solid data from reputable sources is VERY hard to come by, which I found interesting.
I'll also think one reason might be because municipalities report to the FBI UCR on a voluntary basis for their reports, and cities don't stand to gain much from reporting very bad numbers.