The reason the 3 men were water boarded was because it was soon after 9-11 and it was unknown if there were more attacks planned against the US. It is a natural reaction to an attack on your country. A main responsibility of our government is the protection of its people from foreign and domestic attacks.
Torture is against the Geneva Convention in a declared war and against international law in the case of enemy combatants. I don't believe it is mentioned in the Constitution, Declaration of Independence, or the Bill of Rights since these people were not citizens of the US. It is not considered to be a moral way to extract information from POW's.