My preference is to stay in Emeryville. Specifically at the Hyatt House. I'd rather walk the few hundred feet from the hotel to EMY station at 8am than hang around curbside on Mission St in San Francisco before 7am waiting for a bus. Plus, if your westbound train arrives to EMY late you will be glad you don't have a bus ride and long schlep to a hotel in SF.
Install the Clipper app and buy a 1 day Tourist Passport to use if you want to ride the cable cars. There are 3 transit options to get to San Francisco as a day trip:
- Good: Train
Take the train 1 stop EMY to Oakland Jack London Square and then walk to one of the BART stops to take the train. Long walk from Amtrak to BART, or you could take a rideshare. This option won't have rush hour traffic.
- Better: Bus
Take the F or J bus into SF. They both stop about a block from the hotel. Traffic could be a problem.
- Best: Ferry
Take the train 1 stop EMY to Oakland Jack London Square and take the ferry. No traffic, no worries. I think this isn't included in the 1 day pass.
If you do the last option you get 2 tourist sights for free - the ferry ride and the ferry building. From there you can take the historic F streetcar up into the city or around to the Fisherman's Wharf area. Or take the California Line cable car up the hill.
For history buffs, in addition to the ferry, ferry building, historic streetcars and cable cars you could also catch the SF Maritime National Historic Park (2 museum buildings plus historic ships on the Hyde St Pier), and catch a cable car to the SF Cable Car Museum on Mason St. That's also a good place to catch the next cable car, which you can take back to the ferry building area where there are good dining options. Also the Wells Fargo Museum is in the area, if you want to appreciate some pre-railroad history. Last eastbound ferry leaves around 9pm. Check the schedule.
Another thing to catch, probably in the evening on your way back - Jack London's Yukon gold rush cabin and Heinold's First and Last Chance Saloon in Oakland. Particularly if you've spent time at the SF Maritime museum. If it's late and you want door-to-door service it shouldn't be too expensive to get a taxi or rideshare back the hotel from here. But I haven't felt unsafe taking the train back to EMY and crossing over to the hotel by the pedestrian bridge.
If you do this you will appreciate the comparatively lazy departure morning, breakfast buffet at the HH Hotel and short stroll over the bridge to the platform. You will start your ride home feeling fresh and ready to go.
The main thing you miss is the possibility of dinner in SF on the arrival night. But there are some good options near Oakland Jack London Square.