I'm just a gun-toting, bible-clinging joe-baga-donuts fighter pilot who's certainly no expert in maritime operations; however, I don't see this as a particularly difficult problem providing you have a commander-in-chief who's got a couple of brass ones and isn't afraid to be arrogant and act like a bully.
Here's my solution: Have the US Navy sink the "mother ship", where these pirates (aka Merchant Marine Organizers to EIB listeners) launch their attacks on Commercial Ships. These high seas terrorists operate hundreds of miles of the coast of Somalia carry out their attacks in very small boats and need a larger vessel for logistical support. Of course, we would have to show some sensitivity and give the mother ship crew time to surrender and abandon ship before sending it to the bottom of the Indian Ocean. And in the last line of defense, F/A-18 pilots would love strafing a skiff loaded with pirates that gets too close to a Merchant ship.
The problem with this solution is that the current administration sees piracy on the high seas as a criminal offense (not much different than robbing a 7/11) as opposed to an act of war. Fox News analyst and NY Times best-selling author, Dick Morris states that the current administration views terrorism (aka man-caused disasters) as a game of "cops and robbers."