First thing I'd do is a visual inspection of the channel. Open the window all the way and then look from above for any debris.I found two mystery rubber pieces in my '05, about 1/4" long by 1/8" thick(rectangular) and they rattled around...
Ok, after a bit of a closer inspection it seems the rattle is coming from just in front of the moon roof, above where the sun visor sits. If I push up on the ceiling in that area the noise goes away. Maybe I need to take down the ceiling in that area, or just try to shove some foam in there from the moon roof?
I had the same thing. I have my headliner out right now working on a moonroof leak. I found one of the mounting nuts on the moonroof assembly itself loose. I never would have found it without taking the headliner down though. That's not too hard a job, there's a post on here telling how to do it step by step.