The imdb.com indicates that most of the movie was filmed mostly in Texas, with some shots in The Philippines and Mexico.
However, the movie was based upon the story of Ron Kovic's life. And Kovic grew up in Massapequa, Long Island, NY, before and after his tour of duty in Vietnam. It is entirely possible that a few scenes were shot there, but I have no confirmation.
Kovic was awarded a Bronze Star and a Purple Heart medal after the war. Kovic later gave Tom Cruise his Bronze Star medal as a birthday present a year after that movie came out.
Hope this helps!
No offense to Daniel, who did an excellent job in "My Left Foot", but Cruise really broke through as a seriously dramatic actor in "Born On The Fourth Of July".
Cruise also should've won the "Best Supporting Actor" award a few years ago for his mesmerizing and ultimately heartbreaking performance in "Magnolia", for playing a truly creepy and unsympathetic role that he normally doesn't do.
Just my humble opinion.
--It's all on the Born on the 4th July page!!!! Yes, Texas and some others.