I'm not quite understanding all the confusion over where to try a criminal captured in international waters - I think it's actually pretty clear cut and much easier than had he been captured in a foreign land where we didn't have extradition, like say, Somalia. Hence why it's doubly important that the pirates never get to shore. International law gives rights to any signing nation the right to hold a suspected criminal detained in international waters to be brought to the infringed nation without negotiating extradition.
The simple answer to fly him back to the states because the crime was committed against US interests (a US ship with US Cargo and hostile action taken against a US citizen). There really isn't a jurisdictional question here - we just haven't enforced the law in years, but its been on the books forever. The question then becomes federal court in Washington or federal court in NY where most African's are tried for crimes against the US. That question is a simple jurisdiction choice, not one of unknown legal ground.
We also have the option of trying the offender in countries where we have treaties to try criminals found nearby. At one point we had a treaty with Kenya to try criminals found in Africa that we didn't feel were worthy of extradition to America - if that treaty still exists we could do it there, but given the publicity this case received, I don't see the DoJ not bringing this case to America.
Where it does get tricky is if we intercede in a hijacking where there are no US interests (like a French cargo vessel). We don't necessarily have to turn him over to France (why wouldn't we though?), but we wouldn't necessarily be able to try him in America either. I'm sure the Naval Coalition has already worked all of this out, but again as long as he's found in international waters, there is no need to negotiate extradition with the suspected criminal's host nation.
As far as sweetcell's last point - yes, they would most likely have to be in the act, but something as small as impeding a ships progress can be prosecuted.