My '97 did this. Is the area where the vinyl covers the the lower part of the rear window still "well sealed" all the way across? This area is notorious for letting go (glass separating/pulling away from the vinyl) and could be the source of your leak...it was for me. A little test using painter's tape applied before a downpour proved this out.
I tried several things to re-seal mine to no avail. Finally gave in to an overdue top replacment. Now I can put the beach towel that used to ride back there to other uses!!