What year is this set in???
There are some very useful things 'right around the pike', depending one just when this is set...

A Browning 50Cal. on a pintle mount, would be very useful, especially with a larger than normal percentage of tracer rounds, or even some REAL incendiary rounds...

I have read about the sonic gun in 'MAKE' magazine, and it is a nice option, but it is bulky and could probably be defeated by just staying out of range and pelting the boat with bullets, until the crew are either dead or too afraid to go above-decks, or the weapon is destroyed(it is NOT a small target, or something flammable on the boat goes up...

I would suggest a round bottom motor-sailor, with a stabilizer system, like one of the larger Haterois... The round bottom, because you do NOT want to be in a small 'V' bottom boat in heavy seas, the stabilizer, because you do not want to be sea-sick all the time because of the same round bottom design, and the motor-sailor for the obvious reason that you do not want to use all your fuel in the first week...

If price is NO option, there is always those luxury submersibles that that one company sales..
Ahhh, here they are... U.S. Submarines