There''s a pretty nice boat launch on Shelter Island. I don''t know of any ramps at any marinas here though. Also "secure" parking can be hard to find. You might also want to check Mission Bay, I know there''s a few launch ramps there too. Most marinas are pretty full this time of year but the weather is great! Have fun!
P.S. This site: www.sdwaterfront.com has lots of good info on the area