I'll third Lindbergh. One of the largest garages, in a reasonably well patrolled neighborhood. I regularly patronize this station at either end of the schedule (1AM, 5AM) and have never seen less than two uniformed officers either on foot or in cars.

South and West are generally worse neighborhoods, with East being average and North being good. And there's the train switching issue if you go any farther north than Lindbergh.