Jack London Square in Oakland is a great location (especially the access as it's street trackage), but the only freight traffic you see is UP trains headed for the Central Valley via Altamont, or going down the Coast Line. Also, I believe BNSF still goes to Warm Springs once a week, but I don't know which day. There's a fair amount of freight traffic, but not a lot. (Lots of Amtrak trains, however.)
As for Stockton, I wouldn't go there without a car; there's a lot of rough characters around town, and you might need to make a hasty retreat. Stockton's public safety services have been cut way back (and the city just declared bankruptcy), and it's always been the kind of place where you have to keep your wits about you--especially if you're alone and have expensive hardware hanging around your neck. If you like shortlines, the Central California Traction Co. goes to work at Noon M-F at the carbarn on Cherokee Lane (near Highway 99), runs down to the BNSF yard, and then heads to Lodi for lots of switching. The Stockton Terminal & Eastern goes to work at 2pm M-F (enginehouse on Shaw Rd., off Fremont St.), but their line passes through some sketchy neighborhoods.
I would suggest heading to Martinez, about 30 miles NE of San Francisco on UP's line to Sacramento and Roseville. You get all the UP traffic heading north or east from the Bay Area, and several locals and yard jobs originate from the adjacent Ozol yard. Martinez is served by 34 Amtrak trains on weekdays (a few less on weekends), so you could easily go there by train. The area around the station is fairly open for photography, is pretty safe, and has a variety of shopping and dining options.