San Pablo Bay: Actually from the Richmond San Rafael Bridge to the Carquinez Straits there are plenty of areas to fish. My favorites include the area near Rat Rock, the Pumphouse, Pinole Point, the mouth of Sonoma Creek, Mare Island rockwall, either side of the shipping channel, and the flats in front of Rodeo.
Napa River: This can be hot all along Mare Island Strait to the Highway 37 bridge. I also like the Towers and the area between the Southern Crossing and Kennedy Park.
Suisun Bay: I've caught fish anchored where the Glomar used to sit. All along the Mothball Fleet is excellent. I am also fond of Garnet Point.
Montezuma Slough: Due to it's horseshoe shape the Montezuma will usually provide anchorage with the wind coming over the bow. Almost anywhere can be productive. Red Barn, Grizzly Island bridge, the cable crossing, Hunter's Cut, and all the way out the mouth are good places to fish.
Rio Vista: This part of the Sacramento River is popular from the Highway 12 bridge up to Cashe Slough.
Knights Landing: Second Beach is a great spot for large hogs when the river conditions are right.