I had two small leaks on the rear passenger side window. When I say small, I'm referring to only a few drops running down the window in a heavy rain storm, or after I wash the truck and spray soap out of the window channel. I took my '21 Rebel in for a fix and they said the 3rd brake light was leaking, so they replaced it. They were wrong.
I taped off the brake light to seal it and ran a steady flow of water over the rear window on the passenger side. I started seeing small drips on the inside glass, so I knew the issue was with the window seal, or where the cab roof trim attaches. I rolled up a small bead of 3M rope caulk and pushed it between the glass and the body, at the top. I made a mess with the rope caulk, but it cleans up easily with gasoline. I used a flexible card to push the rope caulk tight to the top of the existing window seal. This seal is below the top edge of the glass, so it's not visible from inside or outside of the truck, but it liked to stick to the paint. The gasoline made quick cleanup of this mess and it's completely invisible, but it appears to be sealed now.
The dealer wants to replace the window, which would cost me to re-tint it. If I paid a glass company to fix it, they said they could break it when removing and the cost of a new window would be on me. The rope caulk was the cheapest, easiest and best option for me.