My '99 TJ had a similar noise... for the few months until the engine seized up
. Though it had about 174k miles on it when it did go.
I was already planning on replacing it, so I wasn't about to spend a lot of money on a major repair.
The noise seemed a lot worse under acceleration. Not sure what the actual cause was, but something was definitely rattling in the engine. I had read about cracked intake manifolds - things like that - but could have been anything. Cracked piston, something internal.
Moral of the story... don't let it go too long if it persists!
Sold it to the tow truck driver, and picked up my new JKUS 2 days later.