I know that both are afforded basic rights of a criminal, under any circumstances and referring to them as "enemy combatants" and keeping them off US soil denies them protections that they would have received either as a domestic criminal, or as a soldier fighting in a war.
Even if they're not soldiers in the conventional sense of working under the auspices of another country, they should then be treated as domestic criminals, and put through the american court systems. Both of these routs would enforce protection against torture, and water boarding (if you decide it's not torture), and make those two actions a crime.
Was the Unabomber a terrorist? If so, why was he then tossed into the American legal system? Same with Tim McVeigh. Sure, they were technically US citizens, but then why does the fifth and sixth amendments specifically say
Note that neither of these uses the word "citizen" to denote who the rights apply to. Same with the eighth and ninth amendments in reference to "cruel and unusual punishments" and the "protection of rights not specifically enumerated within the constitution".
In any case, Water boarding is torture and/or Cruel and Unusual punishment. In either case illegal and unconstitutional. And (to yank this sucker back to my original point) has not been shown to be beneficial by a study by the CIA itself, and it's possible it was detrimental to the collection of intelligence by the agencies associated with the programs.