Gotta read these things a little more carefully. I think the OP is referring not to a rattle in the window itself, but rather with the window down and driving next to a wall he can hear a rattle (this was the case with our Highlander after the repairs from the accident, so I get what the OP is saying).
If that's the case, then it could be anything under the truck or in the engine bay (heat shield, etc). I will pitch in with a rattle that was there when I bought my truck. I found the emergency brake cable had a metal connector under the bed that would bounce up over bumps and hit the underside of the truck. Wrapped that metal fitting in duct tape and it's been good ever since. So there's one possibility. But the possibilities could be endless...