Sorry but the Navy does not have a missile firing range off Long Island. The closest Navy range is Wallops Island off Virginia. The Navy would not have a missile firing range under the most heavily used airspace going to and from Europe. Secondly, there are too many people involved in a missile firing. Don't you think that "someone" would have said something?
What happened was there was a fuel leak and the fuel stream went back behind the 747 quite a way. The heat from the engine ignited the fuel from back of the plane and raced up to the plane making it look lit a missile was fired at it.
In any event, it keeps the conspiracy people happy.