Answer:
Two possibilities: Only 'Dan Cooper' knew, or only the FBI knows. If the FBI recovered the briefcase with the 'bomb', they would likely keep this information secret to aid in investigating suspects, which they are still doing.
The fact there is no mention in public records of the whereabouts or disappearance of the briefcase with the 'bomb' could indicate: A. The FBI has it, or B. Cooper dumped it out the rear door of the plane (possibly a while) before he jumped, and it was never found.
I think B is more likely, since Cooper seemed to be a careful planner, and he would want to eliminate as much evidence as possible.