Ferry parking?
http://www.eastbayferry.com/
I am thinking I will have to take the ferry to work on Monday but I have never taken the ferry before. Do any of you know if the ferry has a parking lot? I would have to drive there. Or is there a better way to get from the Berkeley Hills to down town SF?

More info at this
More info at this page:
http://www.eastbayferry.com/what/docks.html
Yes, there is parking -- free at the Alameda terminals and free with validation at the Jack London Square terminal.
Ferry is a good alternative, but there are a number of AC Transit buses that go near the Berkeley hills -- F, FS, G, H, J. Depending on where you are these might be good alternatives. Except for F they only run during the commute period.
http://www2.actransit.org/news/articledetail.wu?articleid=0e529e43
http://www.actransit.org/maps/