So I've own my OEM hardtop for several months now, and just realized the area near the rear window rattling. It almost just sounds as if the plastic is loose, but I can't seen to figure out what the problem is.
Has anyone had problems with their hardtop's and if so how did you get rid of those sounds?

All inputs would be appreciated. Thanks!

 

Rattling or "squeaking"? There's nothing in the HT back there that can rattle, but the rubber seal along the underside of the rear edge of the glass can rub on the plastic trim piece on the car and squeak. You'll need to silicone grease it.
If something is rattling back there, it might be your soft top latches. Are they closed? Duct tape them so they can't move around and go for a drive.

 

first thing you should try is, applying shin-etsu Grease on all rubber parts. then make sure that your hardtop is secured properly. after that, your hardtop kit is installed properly, i.e. rear catcher is not loose. last step but not likely is your glass is loose.

 

Mine made a lot of noise from the rear but it was from the soft top latches. A couple of month after installation, I began to have noise from the front. It was from loose front catchers. I had to use lok tite on the screws to keep them tight.

 

I had and did the same. Pull your visors off along with the plastic piece that runs across the top of the windshield. You should see to screws that hold down the strikers. Those can get loose and could be where you're rattling from, so get some lock-tite. Don't get the strong ones, I think the blue ones are the weakest.