The Jeep Wrangler is a "body on frame" built vehicle. Over time, the body mounts that isolate the body and mount it to the frame and deteriorate. Once this happens, it's common for vibrations to transfer from the frame into the body of the Jeep, and for the Jeep to not quite sit correctly on the frame. The good news is that you can easily replace your Wrangler's body mounts.
You can also install a body lift, to gain some extra clearance for larger tires, without the need to install a suspension lift.