The three most popular locations closest to San Francisco are Crissy Field, 3rd Avenue and Alameda, with Sherman Island a little further east.
3rd Avenue is a more user friendly spot of the San Francisco kiteboarding spots. On a typical NW wind day you will find space in the water, good swell and ramps. Beginners still have to be careful because of the currents and the fact that there is no sandy beach but there are kite schools in this location.
Crowne Beach in Alameda is located in the East Bay of the San Francisco area. It is another good spot for picking up a westerly thermal. The wind is milder than in other locations and the water tends to be flat or chop. The beach is sandy so it is a great spot for beginners to learn and experts to practice tricks. The water gets a bit warmer in the summer so a shorty should suffice during the hotter months.
Other Bay Area kiteboarding locations include Waddell Creek heading South towards Santa Cruz and plenty of other spots along the coast (such as Scott's beach south of Waddell) are great places to catch the surf in peak season. Wave season happens mainly in the spring with the occasional swell coming through in the summer. The waves can get big here so it's best just to watch those advanced to expert riders. It's always a good idea to wear a 4/3 when in the Pacific.
Sherman Island shown in the video below, is a fantastic option for great warm weather kiting when the coast is socked in with fog and clouds. This place is located on the Sacramento River in Rio Vista and it's a place where you can hang out with the whole family and on hot summer days and leave the wetsuit at home. SW wind sets up an ideal side onshore condition. This kiting spot is also good for riders of all abilities.
And if you are looking for adventure and a good road trip ... travel south.
California's Central Coast boasts a couple of good spots to catch the California Kitesurfing action, the list is long: (North to South) San Simeon, Cayucos, Morro Bay, Pismo Beach, Oceano, and Jalama. Pismo Beach and Oceano State allow camping on the beach and sees waves of all size. Jalama is good for all riding abilities and has camping spaces at the state park. The best months for a gusty NW wind in this part of the world are April to June. In these locations you'll find plenty of small to medium sized waves to play on.
Been there, done that, got a question? Tell other kiters about your experience at this kiting destination. You can also embed youtube video if you have something good to share.