I'm not exactly sure what your picture is of, but water entering through the fresh air vent is a common problem with TJ's if the cowl vent is plugged up with leaves and debris. Simply take the cowl off in front of the windshield and take about a 3' rod of some kind (yardstick works) Stick it down through the cowl drain in the center to kind of open the rubber flapper on the bottom, then take a hose with a sprayer and shoot water down through it to flush it out. May or may not be your issue...good luck.
After taking another look at the picture, it appears to be the front of the door opening. If it is, check the tops of your door seals for holes. Mine had a hole where it closed against the hardtop a couple of years ago and water ran through the seal and out a crack in the bottom.