The following marinas offer some transient dockage.  Please call the marinas directly for availability and rates:

SHELTER ISLAND MARINA
(at the Island Palms Hotel)
619.223.0301
http://www.islandpalms.com/media/docs/PDF/marina_brochure.pdf

HALF MOON MARINA
619.224.3401
http://www.halfmooninn.com/resort-services/index.cfm

BAY CLUB MARINA
800.672.0800
http://www.bayclubhotel.com/

There is some anchoring allowed in the Shelter Island area.  All requests for anchoring must be made through the Harbor Police (“Police Docks):

HARBOR POLICE MOORING
(Police Docks)
619.686.6227
http://www.portofsandiego.org/maritime/berth-request-form.html