This is from a little snippet of a YouTube documentary I made about the history of ferryboats on the San Francisco Bay:

https://www.youtube.com/watch?v=duKJ8eNFklI&t=95s

The Western Pacific terminal was one of several railroad terminals that different companies used on the West end of the Transcontinental Railroad. Today, two of them remain as they did originally: This one, which is now offices, and the 16th Street station, which sits abandoned today: https://en.wikipedia.org/wiki/16th_Street_station_%28Oakland%29

Most travelers on the transcontinental railroad who were headed into San Francisco used ferryboats to finish their trip, as there was no rail crossing at the time connecting the rail line directly into San Francisco. The railroads operated their own large passenger and vehicle ferries (kind of like what they have in Seattle today). And the transfer stations were pretty huge and impressive:

https://en.wikipedia.org/wiki/Oakland_Long_Wharf

Today, there is only one subway line connecting the East Bay to San Francisco, and San Francisco still has no Amtrak station. Passengers still have to transfer in the East Bay, but they can either transfer to BART at Richmond or connect to an Amtrak thruway bus at Emeryville to cross the bridge.