Try adjusting the door catch in towards the center of the Jeep, pulling the door in further when it closes. Or try rolling the window down (this is a VERY important first step) and bending the window channel inwards a bit. Not too far as to crack the paint/metal or make the window hard to close, but enough that it sits in a bit further than the rest of the door. I did that on my half doors and it works pretty well. Barring that....foam tape or new weatherstripping. Best silencer I ever did in my Jeep: got the whole damn thing Line-X coated, firewall to tailgate. Carpet? Nah. Just hose it out
I did it for utility, but was absolutely amazed at how quiet it made it. Half doors and a soft top, and we can have a normal conversation going down the highway.