Perhaps it is torture. Perhaps it isn't.
If, however, reasonable suspicion exists that the person is a terrorist (after all, it doesn't physically harm them), then waterboarding is a humane (relative to other methods) way of extracting information, preventing future attacks to save thousands of lives, locating leaders, and weakening the organisation.
I would much rather a cowardly terrorist leader who sends young, impressionable people to their deaths over false ideals to kill innocent people feels that he is drowning for a few minutes, than yet more innocent people are killed by terrorists. The only way to take down al-Qaeda in the long term is to remove its leaders so that the young people of the Middle East can grow up normally and with a respect for human life, without the constant risk of extremist Islamist corruption.