To the original poster...I am with you on this one. I don't care what it is, it shouldn't be making noises like that. Yes, the Jeeps are bricks so I understand the wind noise but after owning so many, I would never let anything like creaking, knocking, or something else like this go just because "it's a Jeep".
FWIW - when I picked up the last Jeep, I had a knocking noise coming from the firewall/foot area. Over 50mph, it got so loud that you couldn't drown it out even with the windows open...as it turned out, some of the push-lock fasteners broke and the fenderwell liners were flapping away.
It will take some detective work but you'll find it. Just like anything else, it is probably something small right in front of you...I was in the engine compartment, under the dash, I pulled the carpet thinking it was wiring, etc.
'01, '03 TJ's
'13 JKU & WK2