Anybody have any recommendations for decent lakes within about an hour driving distance of the Bay Area?
Are you looking for calm, freshwater, or fish?
Calm, I'd suggest the delta or the Estuary.
Freshwater or freshwater fish you'll be looking at lakes, but with low levels this summer, this may be a problem. To answer your question, though, Del Valle, San Pablo Reservoir, Berryessa, Don Pedro, Anderson Reservoir, San Luis Reservoir, Lake Sonoma, and Camanche are all possibilities (some further than others, and I'm sure I missed some.)
Don't be too scared of the ocean; on calm days it's great boating. Even on not so calm days it's usually really good (though the bigger it gets the more you need to know what you and your boat are capable of dealing with.)