Years ago (to me) we use to get permission to remain over night at the
customs dock.

Otherwise preceed into the basin behind Shelter Island and see if you can
find an anchorage for the night. You may be able to get permission to land a
dingy at one of the yacht club docks.

San Diego isn't really very transient friendly. You can sometimes find an
overnight anchorage outside Shelter or Harbor Is. and land your dingy at the
public pier/launch ramp, but I wouldn't leave it there unattended. Same with
the Embarkadaro where the open anchorage is about a mile from the public
dingy dock.

You might ask at one of the fuel docks about overnight tie up.

Steve
s/v Good Intentions