There's some dispute over what waterboarding actually is:
http://www.brendan-nyhan.com/blog/2005/01/what_is_waterbo.html
Just read the article. They say the person is strapped to a board then pushed under water until they think they are going to drown. In my book it makes no difference to me which way it is done. The point is they are not going to drown and the technique works to get them to talk.