Yes, the Coast Starlight.

The main reason I considered Oakland is because we flew into OAK and drove into SF for a few hours layover a few years ago. No experience with Amtrak or public transit in that area though. I will look into San Jose and Caltrain. We have Fairmont points and looks like there is a Fairmont there too, but the reviews are dismal. Thanks for the info and the hotel being uphill from the bus stop in case we decide to go that route.

Thanks for the other suggestions!