I don't know if this will work for you but I sprayed some WD40 on the part of the roof that connects with the car itself, especially the 4 corners where the removeable roof locks in place. I sprayed the car and the roof and the squeaks went away, which was great because they were extremely annoying. Hope that works for you as well
I'd use a silicon spray instead of the WD.
Do you have both tops and the noise only happens with the glass? If so I'd think the rubber around the outside is drying out and shrinking allowing it to rattle. Beyond that, if the glass top wasn't THE one that came with the car it wouldn't be adjusted to the car exactly. I don't remember if the adjustments are on the top or the car.
You have several variables to look at.