The big bomb squad truck is there at the Transbay Terminal right now. AlertSF says you'll want to avoid the area for at least the next 90 minutes.
We'll update with more info as it comes to us.
Update: CBS 5 reports that "San Francisco police have sealed off the TransBay Terminal and surrounding streets due to what they've termed a 'critical incident.' Reports from the scene indicate a suspicious item was found on a SamTrans bus."
Our source at the scene says that "someone is crawling all over a cement truck" inspecting the big vehicle. He tells us that there's a "suspicious package is 'bigger than a backpack'" that's the culprit, or so says a Muni supervisor.
Update 11:48 a.m.: AlertSF says "If you are in that area [Mission at Fremont] you should stay inside and avoid windows and glassed areas." Our source, however, says the cops are being "relaxed" and "casual" about the whole thing now.
Update 12:20: Transbay Terminal bomb threat situation is over. Area is reopening. But please be aware that traffic will be backed up for awhile.