Oru Kayak is based in San Francisco, but I've lived most of the past ten years across the bay in Oakland. It's where I first started to kayak seriously, and while the Oakland waterfront may lack San Francisco's glamor, it makes up for it with its activity and history (and awesome giant machines).
These giant container cranes keep one of the USA's biggest shipping ports running, 24/7.
What was originally a narrow tidal estuary is now a major deepwater channel. The banks are mostly lined with concrete piers, which make great kayak obstacle courses.
It's not all heavy industry and concrete. Jack London Square is not only a perfect urban kayaking launch spot- it has great restaurants and cafes, a terrific Farmer's Market, and a super kayak shop, California Canoe and Kayak. They do tours, rentals, sell all kinds of gear, and are extremely knowledgeable. We highly recommend a visit!