The water cannons do a fine job, the problem is not being able to detect the pirate ships before they are on board or at least knowing it is a pirate ship instead of a fishing ship that happens to be unusually close.
I think anti-tank missiles, torpedoes, the navy seals, 12 inch cannons, cruise missiles, F-22 Raptors, Abrams tanks, helicopter gun ships, and EM non-lethal weapons would all be hugely expensive to equip every ship in the area with and would cause more problems then they would solve.
Bombing their bases? These aren't paramilitary. They have more in common with the Crypts, Bloods and Mafia then they have with the Tamil Tigers. Could you imagine if a barber shop in New York was hit with a cruise missile because it was a base used by the Mafia? You could bet New Yorkers wouldn't be vary happy with Obama after that one.