Do you hear a leaking air noise coming from the seals at highway speeds or is it just a whistling from outside the vehicle that you can hear from inside?
A leaking noise is not normal and means you either have shot seals, which you said LOOK good, or your regulator(s) (or regulator tracks, more specifically) might be on their way out. Lower the window down half way and grab the top part of the glass. Gently pull up and down and try to measure/estimate how much movement you get. If it is more than about 1/8" I'd say your tracks are shot. You can buy replacement Chinese garbage ones from RockAuto or your local parts store, but I HIGHLY recommend Steiger Performance replacements. They eliminate the cheap plastic parts that wear out prematurely with steel and/or nylon parts. You reuse your motor and cable-screw assembly since it works fine (if the window is currently moving) and basically never worry about it again. It can be a bit tough to figure out which kit to buy since it depends on your model year and build date and your drivers side door sticker (with the build date on it) is probably worn off from years of use like most KJ's. If you can't identify the build date you'll have to pray to the dealership gods and see if they bless you with a build sheet that has it. The factory build sheets available online do not list the build date for some reason.
If you're just hearing whistling from outside the vehicle there might not be much you can do other than try some air deflectors and see if they work for you. It could also be coming from the trim around the top of the windshield or the air dam under the wipers. You can play around with painters tape to try to figure out where the whistle is coming from and make a more permanent repair once you find it.
Good luck!
http://www.steigerperformance.com/