According to Wikipedia (not my fave reference, but consistent in this one):
"It derives from the Tagalog word bunduk (Bisayan Bukid) meaning "hinterland", that is, inland area. It also carries the implication that it is "backward" or "unsophisticated"; hence taga bunduk "people who live in the hinterland": i.e., people who are backward or unsophisticated.
Boondocks or diminutively "the boonies" has since evolved into a more general American slang term for suburbs in general, regardless of topology or vegetation."
Fondly remember my "Boonie Hat" in the Army...