From the webpage:
"1) For the missile to be seen, it would need to be an SM-2 or larger. Therefore, it wasn't a terrorist."
It was darkening outside, and surely even the engine of a small missile would have been visible. Some witnesses even described it as fireworks going up towards the plane.
"2) Standards require large launching platforms."
No, some people talk about a small fast-going boat leaving the area directly after the incident. Say a Stinger missile could easily have been fired from a small boat.
"3) Of all the people who saw the streak, none saw the launch. This is strange, given that launch pyrotechnics are much brighter than the engine exhaust. Assuming an over-the-horizon shot means that the missile would be in coast and therefore not visible."
From that far away, the launch would not have been significantly brighter than the rest of the travel path for the missile. See for example: FIM-92 Stinger Surface-to-Air Live Fire Exercise --
http://www.youtube.com/watch?v=av2BzaXF6lg
"4) 98% of the plane was recovered. How could the NTSB, made up in large part of civilians (some of whom would *love* to prove that it was a missile) hide the shrapnel damage? Please do not use Goddard/Rivero's entry and exit wounds unless you want to discuss the splaying of sheet metal in a semi-monocoque structure with an ex-aerospace engineer. I'll win that debate. Hell, I have pictures of gunshot holes that bend toward* the shooter."
The missile hit one of the wings according to the new documentary. Sure, some shrapnel damage would still be found and I think it was in this video (about the new documentary) they talk about holes after such damage: Did U.S. Gov't Lie About TWA Flight 800? Ex-Investigators Seek Probe as New Evidence Emerges. 2 of 2 --
http://www.youtube.com/watch?v=gAkIdb-DUYQ
"5) Speaking of people, thousands would be involved. This would include the ships crew that would know they fired a missile off Long Island right when a plane was downed. How do you keep them quiet? Add to this the civilians who are involved (contractors, etc.) and the incredible paper trail that follows every missile. A hefty number of sailors who were in the service in 1996 have left it. How do you silence them?"
If it was one of the wings that was hit and disintegrated mostly, then hiding the shrapnel damage would be easy, so only a few people would be in on it so to speak. Sure, thousands of people higher up in the chain of command would probably know about it, but they keep quiet because of national security.
"6) Why shoot missiles off of Long Island when proper airspace is available (and no, the warning zone was not hot until after the crash, regardless of what Jim "What, Me Add?" Sanders says)?"
A smaller missile would have limited reach, and launching from a boat is then a possibility since that would reduce the risk of getting caught right in the action so to speak, while operating and preparing the missile equipment.