They're more canon in places than the corresponding books, but also less canon in other areas. Like in the first movie, what happens to Takanuva at the end makes no sense whatsoever, but that's the canon ending, not the more sensible one from the novelization. Stuff like the Rahaga being half-helicopters or the Toa Hordika only having one hand in the third movie is non canon, so as far as the character designs go, the books and comics take precedence over the movie's designs.
But as already mentioned, there's plenty of contradictions all across the media. The first novel, the '01 comics, the MNOG and the canceled video game all contradict each other as well as the original story bible, so none of them are fully canon but all of them contain bits that are canon.