The obvious start is whether is soft top or hard top. Check any sealing surfaces there. Windshield inspect. Turn on water hose and spray at that side and have someone inside to see if can duplicate and locate source.
The Weather stripping at the upper back part of the door is usually the culprit looking at the door staight on is deceptive the seal looks like it's nice and firm agianst the door surrounds but if spray water just on that corner you will eventually notice water droplet on the insdie of the window
I have a 2007 Jeep Wrangler. Every time it rains, my driver's side floor gets all wet. The water is causing my seat bolts to get rusty. There really should be a recall on this problem since many jeep owners are having the same problem. FYI.....I am highly allergic to mold