Had the same type of issue on my 1985 Trans Am. Depending on your year Trans Am, GM has modified the T-Top Weatherstrip, called Second Design, which will resolve the issue. As long as the weatherstrip in good on the T-Top itself.
To have this done is not cheap. They are still avaiable from GM. Right now, there is no one in the NJ area that will touch T-Tops anymore. I have called alot of places, all say noto T-Tops !!
One place recommended a place in Bristol PA that handles T-Tops Exclusively:
http://www.eastcoastt-top.com/index.html
After speaking with him, he is very knowledgable on T-Tops and has all parts available that you will need. With any specialty shop, the price is going to be high.
My Tops do not leak, but the Center Bar is becoming loose and I hear the wind with the T-Tops on the highway. I plan on bring him the car to resolve these issues. Price Quoted was around $1100.00. New GM Weartherstripping, Center Bar, Replace any worn Parts on T-Top Itself, adjust/realign Tops, Water /Wind Test ect. They need the car for 2 days, they repair, replace and test prior to any car leaving the facilty, and is guaranteed
Hope this helps you out