Looks like Michael Bay was misquoted when he said the TMNT reboot would have the turtles be aliens and not mutants. According to an interview he did with Moviefone:
“There was that quote saying that we’re making [the Ninja Turtles as] aliens. We’re not. It’s the ooze! It’s from the original source material. These are from the original writers, and I never went out to correct myself in the press. I do listen to the fans and I do want this to be authentic. I think they’re going to be really happy with this movie. When I see the digital stuff, the turtles look great.
Really Bay? Really?!? via The Mary Sue.