Leaks in the side window seem to be common. You need to see if the water is finding its way round the edge of the glass or the metal aperture. Running a hose on it for a few minutes should do the trick. Mine was getting into the seal at the front edge, then running down to the corner and coming in along the bottom over the top of the seal. A tube of sealant with a small nozzle run under the front edge between the seal and glass stopped it.
'08 Chrysler 300CRD (MB OM 642 engine)
'95 E220 estate
'89 230TE (R.I.P.)