There are no boat excursions - it's a high security military base, which is tightly controlled and staffed by the Navy. Your options are to fly or take the ferry from Maui to Oahu. But since the ferry takes longer and can be rough, flying would be my first choice.
The way it works is that people line up at the park gate starting about 6:30 a.m. for timestamped tickets. The ticket is for the launch that takes you out to the Memorial, in the middle of the bay. They only give out a certain number of launch tickets every day, and if you get there late on a popular day, you may not get a ticket at all. They open the gate around 7:30 and then you can go in and tour the museum, bookstore, etc. When it's your time for the launch, you line up for a mandatory film, and then you go out on the launch with your group. You are out there for 20 min. or so and then back to shore, where you can wander around some more if you want.
We visited in June or July and got there by 6:30 and there was already a line. When we first got there, it was cool and uncrowded. By the time we came back on the launch, about 10 a.m., you could barely move through the crowd, and it was hot and sultry. So my advice is to get there before 7:00 and beat the crowd and the heat.
A couple more things:
They have a dress code for visiting the memorial.
You cannot take ANYTHING into the park with you, including purses, backpacks, fanny packs, diaper bags, or camera cases. You can take anything that fits in your pocket and a camera, in hand - that's it. There is a "for-pay" place to check your stuff in the parking lot, but I personally wouldn't want to leave my purse out there - it's not run by the Navy. I locked my purse in the hotel safe, and just put my ID, credit card, and some cash in my pocket.
The park website -
http://www.nps.gov/usar/planyourvisit/index.htm
Here is the Super Ferry website -
http://www.hawaiisuperferry.com/schedules/default.html
The ferry takes about 3 hours - it's less than an hour to fly. (It's 93 miles from Kahului, Maui, to Honolulu, Oahu.)
Depending on the day, the fare is $49 or $59 for adults, and $39 or $49 for children - one way. Which makes the ferry about the same price as airfare, for a 3X longer trip, which may be rough.