Any of the stations in central Contra Costa would be fine (Concord, Pleasant Hill, Walnut Creek, Lafayette, Orinda). They should all have plenty of spaces after 5pm. I parked at Walnut Creek when I was in the City 2-3 weeks ago, and was there overnight without any problem. There will be a lot of people on the trains into the evening hours.

Some of the stations require you to punch your space number into a validation machine once you are in the "paid" area (Walnut Creek does). There is no charge (yet) for parking in Contra Costa.

The last train out to Contra Costa leaves just after midnight from downtown San Francisco. It will be a "Bay Point/Pittsburg" train.

The Embarcadero station is literally at the front door of the Hyatt Regency Embarcadero. It will be the first stop after you come out of the 7 mile Trans Bay Tube.

Trivia: I used to work for BART in their police department.