JFK,Jr. had very few flight hours. So few that his last instructor pilot was so concerned he offered to make the flight with him that evening/night. The offer was rejected.

In the latter stage of the flight haze and darkness made it impossible to distinguish an horizon which called for flying solely on instruments. JFK, JR was not an instrument-rated pilot. It is highly likely he became spatially disoriented due to his inexperience flying under the conditions the aircraft encountered and inadvertently flew the plane into the sea.

When the entire scenario is taken into account pilot error is the most likely and convincing cause of the crash.