I was on Westhampton beach that day and saw TWA800 explode. I don't buy a ground launch SAM theory. If TWA800 was indeed shot down by a missle it would have most likely come from the air. Even more likely is that a bomb was on board.
To shoot down that plane at the distance it was at and current atmospheric conditions, you would have needed a fairly sophisticated guidance system (not heat seeking or optically guided) with enough range -- certainly nothing very portable or easily hidden if on board a ship.
And if you ever saw something like an SM1 or SM2 being launched from a Navy ship there wouldn't be any question. It's quite a sight!
http://www.fas.org/man/dod-101/sys/missile/sm-2.htm
The "Ceiling" of the Stinger is Only 1.8 miles
http://www.fas.org/man/dod-101/sys/land/stinger.htm
SA14 (The USSR's Replacement for the SA-7) its ceiling is also 1.8 miles. Introduced in 1978
http://fas.org/man/dod-101/sys/missile/row/sa-14.htm
The SA18 is the Third Generation heat seeking man portable missle
http://fas.org/man/dod-101/sys/missile/row/sa-18.htm
THE UK has supplemented its Stingers with Blowpipes/Javelein/Starstreak series of missles. Unlike the Stinger and the SA-7, 14 and 19 these are opitcaly guided missles, not heat seeking (With the Starstreak riding a laser beam to the target)
http://fas.org/man/dod-101/sys/land/row/starstreak.htm