Please keep in mind that the AMTRAK thru bus going to SF from Oakland station, does not go to Fishermans Wharf. I believe that you will have to get off at the Amtrak office near the Ferry Bldg. in SF. You will then need to get on the MUNI Railway system to get to the Fishermans Wharf area.Another thing to keep in mind is that the CS usually pulls into Oakland at about 7:30 PM (If it is on time), this would mean that it would be close to 9:00 PM by the time you arrived in the Fishermans Wharf area. I believe that things start closing down there at around 9:30 or 10:00 PM.
To be on the safe side, I would plan to check in to your hotel or motel when you arrive in SF, and then go to Fisherman's Wharf area the next morning.
It is usually a very plesant expierence to walk around Pier 39 and Fisherman's Wharf at about 9:00 AM due to the fact that there are no crowds there yet and everything is opening up around that time of the morning.
Hope that you and your daughter enjoy your stay in SF.