As an early morning runner in SF, I see coyotes in SF every week or two, including at Twin peaks as mentioned in the article. One morning in Golden Gate Park I warned a few people walkings dogs since there were about 4 coyotes around the corner. From my first hand experience, I'd assume any wooded area with cover in SF has a coyote living there.
They were pretty small though. I wouldn't want my Yorkie near them, but they were more like an oversized Fox.