On a TJ, I always run the wire behind the hinge, and then behind/under the cowl. From inside the cowl area, there is a hole you can pull your wire through to get to where ever your relay is (if you can't find the hole, you can drill your own).
In this pic, you can barely just see the wires on the right of the hinge. In person, you have to get that close to see it.
IMO, it's the cleanest wire routing.