I kept my boat in Alameda and commuted to it when my son and his family
lived in the Bay Area. When they moved to Carlsbad thought I'd just move my boat south but ended up sailing it home because of the unavailability of slips in Oceanside. When I checked last year, the waiting list was close to ten years. Believe you can buy a boat already in the marina and keep the slip, however. Don't know about live aboards.
In San Diego, a couple of new marinas have come on line and the poor economy has eased the slip situation. Slips were expensive, though, almost twice the $300 a month I was paying in Alameda. San Diego is also almost an hours drive from Carlsbad. You'd be going against the rush hour traffic so might be able to cut that time down. My Daughter in Law works in Downtown SD and commutes via the train. If your husband's new work place is close enough to the train station so he can walk or bike, it makes for a rather pleasant commute.