Originally Posted by adventurepdx

This. It's nice that Amtrak offers Thruway bus service from their East Bay stations into SF, but if you have a bike it's more of a hassle then a convenience. You can take the BART across the Bay, then it's about a two mile ride from MacArthur BART to Emeryville Amtrak (the station where most of the Thruway buses use). Oakland-Jack London Square Amtrak is less than a mile from either 12th Ave or Lake Merritt Stations. And as mentioned above, the Richmond BART station is directly across from the Richmond Amtrak. Though I will point out that only the California Service trains (Capitol Corridor and San Joaquins) stop in Richmond. If you are taking the California Zephyr, you'll need to use Emeryville. (You can use either Emeryville or Jack London for the Starlight.)

And yes, the ferry is another option. You can take a ferry from SF Ferry Building to Jack London Square and the Amtrak station is right there. And the ride is a lot more scenic then the Transbay Tube.