One Aviation Week article from several years ago quoted a classified report that Flight 800 was on the very outermost edge of the "footprint" of even the best shoulder-fired missiles. There's no direct view of the exhaust, and the missile would be almost out of fuel before it got to the aircraft. Hardly an attack that would provide a high degree of confidence.
It's known that the forward section of the aircraft was instantly sliced off from the rest of the plane. That's why all voice, data, and black box recordings stopped instantly. A smaller plane, hit by a full-sized SAM, would still be functional enough for the black boxes to continue working, even for a few seconds. Unless it was hit with enough explosives to shred the entire aircraft instantly (like some of the demo films of missile tests against drones). You could blow the wing off a 747, and there would still be enough time for a mayday, and continued recording on the black boxes.
The same article mentioned that there was one incident of a center tank exploding on a jet airliner (tens of thousands of jetliners of all kinds, not just 747s). It happened on the ground, and there was enough evidence to show it was caused by a combination of major damage to high-voltage wiring passing through the tank, and just the right fuel-air mixture in the tank. Jet fuel is far less volatile than gasoline, and you have to work really hard to get the right fuel-air mixture, and a strong enough spark. It's like trying to get an explosion from diesel fuel.
The only method to produce the acknowledged evidence of instant "decapitation" (previously unknown in all of aviation history) is a high-powered explosive placed on and around the join section where the forward cabin is attached to the main body of the fuselage. Five to ten pounds of Semtex would start the process going, with aerodynamic forces finishing the job a few milliseconds later.
The implications are more dire than having someone on a boat shooting at you. It meant someone with engineering knowledge would have to get explosives inside the aircraft, and placed at the one location where it could provide a kill with a high degree of confidence.
IMO, the "exploding center tank" is pure BS. Based on what we've seen in Iraq, a MANPAD does not provide a high enough degree of damage, and it strikes a rear wing edge, or an engine, not the middle of the fuselage. Even aircraft hit by full-size SAMs do not go down in the manner of TWA 800. That leaves only an energetic explosive planted in exactly in the right spot by someone with access to the innards of the aircraft.
Yes, I have seen similar data, especially expressed as an envelope of altitude and distance. If you are outside the envelope, the missile can’t reach you. So, this does weigh greatly against a MANPAD, but there are other missiles that would be capable.
Even so, just the attempt of an attack, even if it was made where the aircraft was outside the MANPAD’s operating envelope, would have a significant meaning both to the public’s perception of safety and to the necessity for a military response. Could the attack have been made closer to JFK where the aircraft would have been lower? I tend to think that making an attack in broad daylight where there would be lots of witnesses to the launch is the signal the jihadist wanted to send the Great Satan and if they actually succeeded at hitting the target, all the better.
Even so, the Clinton Administration decided to treat a jihadist attack as a crime and not as an act of war, thus adding to the evidence that lead to bin Laden deciding he could go ahead with 9/11 and the US would not respond.