The NTSB had come out and said it was a fuel leak that was ignited by the heat of the engines that caused the explosion. The report stated that a stream of fuel was ignited far back of the plane and raced up to blow the tanks. That made it look like a missile was coming up from the rear.
Finally, when has the Navy ever conducted missile firings off Long Island??? Is there a test range set up below the flight path of planes flying to Europe from JFK???
The only live-fire SAM range that I'm familiar with on the East Coast is a NASA installation called Wallops, off the coast of VA. I don't know if it has ever actually been used. All other SAM ranges (close to or on CONUS) are on the west coast.
The NY-Europe corridor is one of the busiest flight corridors in the world. The Navy would never conduct missile exercises in the LI Sound. It's ridiculous.