I would reccomend a charter out of Emeryville sportfishing, or possibly halfmoon bay, which would be Huck Finn Sportfishing.
Right now, they have offshore salmon, and halibut and striper fishing in the bay. Lots of opportunities for good fishing. Check out www.coastsidefishingclub.com (you have to register to see the boards) and check out the discussion boards to see the current info. Pretty much just a saltwater site though.
Not sure about bay area freshwater fishing. Theres the sacramento river (pretty far), nothing happening there this time of year, maybe schoolie stripers. San Luis Reservoir, but that's pretty far too, and a hit or miss striper fishery.
If you just have a few hours, go to the pacifica pier, they should be getting some perch there.
Better Still you can catch a party boat fishing trip that goes out under the Golden Gate Bridge and these days about 20 miles out and they are catching chinook limits daily. Weekly report here: http://www.sfgate.com/sports/outdoors/fishing/
The best captain in the fleet, bar none, is Jackie Douglas, skipper of the Wacky Jackie 415-586-9800. Call to make a reservation.
The SF fleet docks right at Fisherman's Warf, you get there about 5:30AM and spend a good day fishing.
Check it out -- you wont regret it. How many people do you know who have been "under" the Golden Gate?