This is an excellent post and I think gives a very real scenario for a ferry hijacking. Load a truck bomb on the ferry and steer it at full speed toward a carrier or perhaps a cruise ship. The carrier commander then has the Hobson's choice of firing on the ferry full of civilians, or sustaining damage to his ship.
I remember during the military base closing arguments a while ago that many naval officers thought it was a big mistake to close Alameda Naval Air Station (San Francisco Bay) and relocate carriers to Bremerton, Washington. Naval ships on Puget Sound have to navigate over a hundred miles of inland waterways before they hit blue water ocean. At Alameda it less than 10 miles. They are much more vulnerable to attack in Puget Sound.
An Islamic attack resulting in several thousand deaths and severe damage to a naval ship would be a huge coup for their cause. It would likely result in in Bush being boted out next election.
I agree, Puget Sound is also closer in the event of Nuclear attack since it is closer (farther north). It is within range of Chinas missiles Alameda was not.
As for the ferry attacks, I don't know if passengers have access to their vehicles or not, but even if they don't a concealed hand gun could take care of the guards. After that Arabs coming aboard in ones and twos could go to their vehicles and get rifles and even machine guns out of their trunks. They are not searched.
Take the bridge and they have effective control of the ferry. There would probably be people jumping over the sides after that, but as big as these ferrys are half would probably be knocked unconscience from the fall.
Some snipers with 30.06 w/ scopes on the bridge could keep any potential rescuers away, and the cold water would kill many before help arrived. The news helicopters would be kept back that way too but they would still be close enough to film a missle attack by the National Guard Jets.
The carrier captian would probably not get authorization to fire until the ferry was under his effective target zone (too close). I expect he would order abandon ship except for essential personnel. (fire crews etc.)
It would be a big show for Al Quaida.