FWIW, some thoughts other places worth considering a visit: Paradise Cove for overnight anchoring on the east side of Tiburon and just north of Angle Islandís Ayala Cove; San Rafael channel Ė two on the water restaurants Pier 15 and Terrapin Crossroads (GreatFull Dead restaurant venue) and San Rafael Yacht club transient dock space, with easy access to down town, just be aware of thin water at low tide. China Camp just north of San Rafael for overnight anchoring, itís a great jumping off point for heading east to the delta.
As already mentioned Benicia is also a good overnight spot with easy access to down town and good restaurants. Rio Vista, up river on the Sacramento main channel has an excellent harbor for over-nighting; if anchoring out is your preference Horse Shoe Bend behind Decker Island is an excellent spot that is protected from the prevailing westerly winds, itís approx. 2 KNM down river from Rio Vista. From either Horse Shoe Bend or Rio Vista you can choose to either go up the Old Sacramento River, or up Steam Boat Slough, (have breakfast at the Grand island Mansion) and then connect further up river on to the Old Sacramento River, which in turn gives you the option to loop and head back down river and visit Isleton and other points already mentioned. Or leaving Horse Shoe Bend / Rio Vista turn east at 3 Mile Slough go past Brannan Island State Park and head for the San Joaquin River toward Stockton. Off the San Joaquin before Stockton you have the opportunity to travel up the Mokelumne River and stop along the Delta Loop at Moorís River Boat, Willow Berm Marina or others; and from there to must see Georgiana Slough, or if really adventurous head up to the Meadows Slough. Or continue east along the San Joaquin toward Stockton. So many places and so little time, no matter where you choose to go you canít go wrong with any of the options everyone mentioned.
A good read for places and things to do in the delta is the Bay & Delta Yachtsman Magazine at YachtsmanMagazine.com
Also, when heading out of the delta back to SF, stay out of San Pablo Bay in the late afternoon on an ebb tide, especially if there are 20+ KN westerly winds. Very short duration, steep 5í to 6í or more square waves, are not unusual and not fun.
By the way when heading north from Santa Barbara if needing places to hide out from the weather consider stopping at Port San Luis / Avila Beach, they have anchorage buoys; and north of Morrow Bay at San Simeon. After San Simeon you are on your own slugging it out until Monterey. Charlies Charts for the Pacific Coast is a good source for ports and land fall options along the coast. Did this trip a few times in a 53í Hatteras from Vancouver BC and back; its fun if the weather is cooperative and you plan the passage around Mother Natureís schedule. Enjoy your trip!