I've been twice, and I think I'd base my decision on whether to take an all-day tour with a company or DIY based on whether I had a car. With a car, I'd just visit the websites of both the AZ and the USS MO and book convenient times online as soon as I had my dates pinned down. Afterward, if you feel like it, you can visit Punchbowl Cemetery as well.
Also, if it's early in your vacation and you're coming from the mainland, remember that Hawaii is several hours behind us, so early tours are quite doable as you'll probably wake before dawn anyway. (If you have a 4:30pm flight, definitely book the earliest tour.)
If you book a tour of the Might Mo as well (might as well, as they share the same parking lot), allow several hours to Pearl Harbor, as you may want to linger at the memorial (it's very moving) and/or browse the grounds and bookstore/musuem. Often tours don't leave time for this and it's a shame because you need time to absorb it all.
I've found that behind-the-scenes tours are usually worth every dollar, so if you have an opportunity to book upgraded tours (e.g the Jamie Lee Curtis movie or a behind-the-scenes tour of the Might Mo), do it. You'll be the envy of the folks walking around trying to listen to the headset tour.
Now, on the other hand, if I didn't have a car, I'd probably opt to book with a tour company for sheer convenience as they usually offer pick-up/drop-off from hotels. Not renting a car can save you up to $100 a night (rental cost + hotel parking), so decide what sounds best to you and go with it.