Angel Island State Park, across from Tiburon, is a must-stop for anybody visiting the bay. It has a very nice hiking trails that have some awesome views of the bay. You can even camp on the island, although I never have.
The last time I visited, there was a nice little bar/convenient store. You can grab a mooring ball for a fee (not sure what it is nowadays) but you cannot stay overnight at the docks or come ashore after hours. Ayala Cove is generally pretty sheltered from the winds and Racoon Straight is not normally too rough.
