Have you checked the taillights themselves?
Since the taillights are grounded to the body, often times if you have a rusted body or taillight guards, the ground points for the taillights won't be good, and then the brake lights won't work. Although if that's the case, usually nothing else will work either (i.e. turn signals and parking lights), but it's still worth checking.
The other obvious thing to check (and PLEASE do this) is the brake light bulbs themselves.
I find in situations like this, usually it's the very simplest answer that ends up being it. Occam's Razor basically.