If you're going to be leaving from San Francisco, a good way is to take the Amtrak bus from the Ferry Building to Emeryville. Richmond is also a good option, but you miss some interesting trackage. If the times work out, you can take the (infrequent) ferry from the Ferry Building to Oakland and walk a few blocks to Jack London, which gives you the street trackage on the Embarcadero (the Oakland one, First St. in more prosaic times), and with luck meet a train of double-stacks in the middle of the street. The way I like to do it is to take BART (Fremont or Dublin-Pleasanton) to Oakland Coliseum. There is a covered, elevated walkway from the BART station to the Coliseum itself, and a stairway opening off it which leads directly down to the Amtrak platform. Trains from San Jose stop there, and unless the schedule has changed since the last time I looked, there is a morning arrival from Sacramento which turns at the platform and returns to Sacramento. You can sit anywhere you like. You can see New Haven-style catenary supports dating from Interurban Electric days (they're also visible from BART on your way there), and you'll be comfortably seated when boarding begins at Jack London. After the street running you can see a lot of active yard trackage, and as you swing to the right you're passing Desert Yard, so called because there was no water supply (and this in steam days! -- I've read that any engine sent to do work in Desert Yard had to make sure of a full tender, and get itself back to a water plug before going dry). Somewhere off to the left is where the tracks went west to the Oakland Mole, from both the Sacramento and San Jose directions. Shortly thereafter is the former Oakland 16th St. Station, a considerable distance off to the right, away from the tracks. It was structurally damaged in the Loma Prieta earthquake and had to be abandoned, and since then highway construction led to a track relocation placing the railroad well away from the station. (In fact, if there's been redevelopment, it may not even be there any more.) More passengers will board at Emeryville. Shortly before Richmond the BART line comes in from the right. If you board at Richmond you'll have missed everything so far. Soon after Richmond you can catch glimpses of the paralleling Santa Fe route to the San Joaquin Valley. On your left from here to Martinez you have a great shoreline view, with a good many meets, since the Cap Corridor is now almost hourly, and you have the San Joaquins in addition. At Port Costa there are pilings in the water which I have to believe are the remnants of the ferry slips dating from the days of train ferries from Port Costa to Benicia, which lasted until the bridge was built at Martinez in 1930; you'll cross it right after leaving Martinez. The Overland Route, which you're on, rises in the center leaving Martinez, with a flying junction to the San Joaquin route on either side. (Trivia question: is this the only flying junction in the U. S. west of Chicago 68th St. (?) on the formerly IC Metra Electric?) Things get more routine after this, but there is an interchange (on the left) with the Northwestern Pacific shortly before Suisun-Fairfield. At Davis there is a wye junction with what used to be the main SP passenger route to Portland up the west valley. You enter Sacramento over the "I" St. bridge (rail on the lower level, highway on the upper). Immediately to the right as you come off the bridge is the California Railroad Museum (a must if you have time), with a rail connection which is normally severed but can be installed for equipment moves -- that's how they got 4449 into and out of the museum for the sesquicentennial in 1999. I gather from recent posts that the Sacramento station is pretty well torn up because of a major track relocation which straightens out the tracks by putting them farther from the station.
The seating is pretty well open -- people just get on and sit down. I've found the return trains well filled out of Sacramento on a weekday afternoon. Try if you can to get a train that arrives in Richmond before sunset -- it would be a shame to do the waterside running in the dark. If it's going to be after dark, you might as well be ticketed to San Francisco; this will give you the bus ride from Emeryville (and since westbound traffic on the Bay Bridge uses the upper deck, you get a nice view of the City if you can grab one of the front seats on the right).
There is a cafe car, and the food is OK. Double deckers (so-called California Cars) are usual. Don't know about wi-fi.
You'll enjoy it.
