San Diego is certainly a hub of Naval vessels on the U. S. West Coast. You can expect maybe 4 Navy ship movements in a given day, and lots of small military boat activity. Weekends are more quiet than weekdays. Merchant ship traffic is minimal. In late afternoon, Shelter Island (actually a peninsula accessible by car) has good lighting for ships passing in the channel. In the morning, Embarcadero Park South or the mole at Cesar Chavez parkway (still called Crosby Street on some maps) is good lighting. But more than anything, I recommend the harbor cruises. They see just about every military facility in the harbor. Although one trip is expensive, for about twice that price (about US $50) you can buy a year-long pass from Hornblower. The other tour company is called Flagship, and both leave from the same spot near the USS MIDWAY museum, which is also worth your time and money. Both companies offer just about the same cruise at the same times for the same costs, but look for special fares online.
Up in the Los Angeles area, you won't see any Navy traffic anymore, but there's frequent merchant traffic. In the Long Beach side of the harbor, there are presently no "legal" photo points of any value. On the Los Angeles side, there's not much legal for morning traffic, but afternoon traffic is great from three points. Near the LANE VICTORY out at the end of Miner Street is great if it isn't blocked off for special events. Near the Pilot Station at the end of Signal Street there's a walking pier that is right on the channel. And although it may change, there's lots of parking and little conflict at what used to be Ports-o-Call, a failed tourist district on the channel along Sampson Way (continuation of Harbor Drive).
The bulk of Los Angeles traffic are container ships, which normally arrive before the start of the day shift (so well before 8 AM) and sail well after it (so after 4 PM.) You'll double your number of ship movements if you go to Los Angeles during the summer vs. the winter. -George