I think some kind of electrical fire. That would explain why systems were shut down. It would also explain the last recorded turn as the pilot tried to get to the nearest airport that could handle that size plane. Smoke/fire probably got serious enough to realize they couldn't make the airport and had to ditch the plane in the ocean, much like the plane in the Hudson River. He may have put the plane down somewhat successfully, but with enough damage that the plane soon swamped and went down virtually intact without a debris field.
...or again, Aliens.
