If your bike is being shipped before you get on the train, then look into catching an Amtrak connector bus to Emeryville. I know it stops by the Ferry Building (an easy streetcar ride from Pier 41), and I think it may also stop in other parts of town. But as I said, Pier 41 to the Ferry Bulding is an easy staright shot on the "F" line, which is serviced by a collection of old trolley cars from various cities that SF bought and fixed up to appeal to the tourists who frequent the Fisherman's Wharf area.
This should be the link for the "F" line -
http://transit.511.org/schedules/ind...pe=6098&cid=SF
You will be going "outbound" and catching the trolley at the Beach and Stockton Streets stop anbd getting off at the Embarcadero and Ferry Building stop - according to the schedules, it's an 8 minute ride. (The schedule shows the Beach/Stockton stop, but not the Ferry Bidg stop, but the Don Chee/Steuart St stop is the next one past the Ferry Bldg stop, so computing the time is easy.)