USS Midway is a must do. Even if your wife isn't into military/airplane stuff the view from the flight deck overlooking the bay is simply amazing. The SD Maratime Museum is mediocre. I dubbed it the SD Museum of "Floating Junk" because so much of it is in a decrepyted rusting/rotting state. But the Soviet submarine is pretty cool, only one of its kind left in the US that you can go inside of IIRC.
The other thing I would highly highly reccomend is the Harbour Boat Tour. You get to get within a couple hundred feet of some of the most sophisticated military equipment in the US's arsenal. I even made a photo montage video of the Harbor Tour.