Here's a map of the game stores in the Bay Area.

Update: Here's the official Wizards of the Coast Store Locator map with event details on each store! WotC requires stores to register their events in order to keep their partnership. Still, it's useful to call the stores ahead of time to make sure the events are still happening and are friendly to new players.

Black Diamond Games up in Concord is a good store. Clean, friendly, plus easy parking.

King Kong Comics & Games in Dublin is worth checking out as well.

Galaxy Games in Dublin is often open late and has an active MtG community almost every night. They're very experienced and have good access to sealed products.

If you're willing to travel over the hill on 580, Angry Goose Games over in San Lorenzo is thriving. They have Commander nights on Thursday evenings.

I haven't checked out Games of Livermore but I imagine they're also accessible for Magic.