We took the two hour North and South harbor tour. The guide gave a thorough and interesting narrative of the ships and surroundings. There was a little problem with the PA system, but he worked quickly to rectify that and made sure we could hear. I've read some reviews saying to be sure to get on one particular side of the boat for the best viewing, but we didn't find that important. We stayed on the top deck and could wander around for the best photos. We had good weather, which helped a lot.
This company gives a $5 discount for holders of a USS Midway Museum ticket. The website didn't have a function to claim the discount, but when we showed up with our prepaid harbor cruise tickets and the previous day's Midway tickets, the ticket office credited our credit card for the discount. We recommend this tour to anyone interested in the harbor, but if you can do only the north or south portion of the tour, we'd recommend the south leg.