According the Chron they are native to the area and moving back in after having been killed off in the last century. We know where they come from: a surveillance camera has picked up one immigrant crossing the Golden Gate Bridge at night.
Apparently we are most likely to see them when they are defending their cubs. Here's a picture from the Chronicle the three little ones known to have been born in the park this year.
video of a Rottweiller encountering coyotes with young.