Sausalito, Tiburon, Richardson Bay, Racoon Strait and Angel Island are probably the best place to paddle in the bay area for intermediate and advanced paddlers. The view is to die for with Golden Gate Bridge and San Francisco Skyline in the background. The wildlife in Richardson Bay is abundant with sea lions, harbor seals, large variety of winter birds and sometimes you might even see porpoises in Raccoon Strait. Angel Island has some spectacular campsites. The kayak camp site is on the northwest side of the island sheltered from the prevailing wind from the Golden Gate Bridge. A short walk to Camp Reynolds will give you a nice panoramic view of the city, Golden Gate Bridge, Marin Headlands, and Mt Tamalpais. Racoon Strait between Angel Island and Tiburon is a very special place because when the San Francisco Bay was not a bay (the ocean level was lower), Racoon Strait was a canyon that the Sacramento river has cut through with the Golden Gate as the mouth of the river. During king tide events and winter/spring run off periods, the river can still be seen from Angel Island. And with the massive ebb tides, so come the standing waves - super fun!
On January 13th, I paddled from Bluerush Paddlesports with Jen Fuller to Strawberry Point near the Audubon Society. Then I paddled along Tiburon, crossed Racoon Strait and camped at kayak camp. It was just after a big storm and it was incredibly clear after the fog had disappeared. The king tides were in while I did a hike around Angel Island and got some really nice pictures of the Strait as a river. I also played in the riptides after the hike as the runoff was especially strong. It was great fun playing and surfing with just a minute of commute.
Put-in: There are multiple places to put-in at Sausalito. There's a public ramp next to the restaurant Salito/Bar Bocce - parking can be difficult to find there. There's the public Dumphy Park and a nice little beach favored by kayakers and paddlers. There's also another public beach and a dock near the Bay Model.
Take-out: The kayak camp on Angel Island is on the northwest side of the island between Ayala Cove and Point Stewart. There used to be a cable crossing between Angel Island and Tiburon. The kayak camp trail is just behind the cable crossing pilings. It can be difficult to spot but if you see the black rock beach, you've gone too far. The trail is steep and you'll need to bring up your boards to about 100 feet up the trail where there's a clearing. Definitely do not leave your board on the beach because at high tide, there's no beach. Also with ferries and other boat wakes, the waves can reach pretty high up the beach above the high water line. The camp is awesome with lots of flat space, bear box, picnic tables and a bbq rack (no wood fires, coals only).
Hazards: Racoon Strait can definitely be an intimidating place to paddle due to the fast current and boat channel. Wind and fog can be an issue here so close to the Golden Gate Bridge.