Big question: Are you planning on checking baggage while aboard the train?
If you are, then I would recommend doing the following.
- Ride the California Zephyr all the way to Emeryville.
- Search around on-line to find out which of the three SF Bay Area airports are offering the lowest return airfare back east: San Francisco, Oakland, or San Jose.
- PM me with your choice of airport, and I'll help sort out where to stay and how to utilize the local public transit to get where you need to be.
If there is no checked baggage while aboard the train:
- Ride the California Zephyr to Richmond (RIC) which has a direct link to BART which can then be used for accessing either Oakland or San Francisco airports.
- San Francisco has a BART station inside the terminals, which makes it the easiest airport to connect with.
- Oakland has a small bus bridge between the BART station and the terminals; extra $3 (correct change only, either Cash or a BART ticket with $3 on it. If the BART ticket has more, you'll loose it as you won't get your ticket back.)
- San Jose is by far the more difficult airport to access, but it can still be done either by Amtrak Capitol Corridor or CalTrain to SJC, then lightrail to the airport station (about a 45 minute ride) and then a bus bridge to the airport.
*EDIT* I'd make mention of Sacramento airport, but there is virtually non-existent public transit between it and the Amtrak station. You would need to make arrangements with a cab or airporter (or get a hotel that has a shuttle.) Additionally, SAC tends to be a pricier airport to fly from, and you'll likely connect somewhere (very few direct flights to points east of the Rockies.)