Originally Posted by
returnoftheyeti
You might consider staying at the Waterfront Hotel in Jack London Square. Its right at the train stop. You will be able to get food, get right into a room. In the morning you can see some of Oakland if you wish. BART is a short walk, you can Uber, or even take a ferry into San Francisco.
my .02
I totally forgot about that place! My wife and I were walking around there right before a Yoshi's performance. We were thinking that we would recommend the hotel to visitors. It looks like a decent place (nothing fancy), and it is right there at the ferry terminal. The ferry ride itself to S.F. is like a tourist attraction, and it takes you right to the ferry building throughout the day, and also to Pier 41 in the am:
http://sanfranciscobayferry.com/route/alameda/sffb.
This would be ideal for the OP. Forget the Amtrak bus, taxi/Uber, etc. Walk off the train, go to the hotel, get some rest. Take the ferry into S.F. the next morning.