Water Leaking Inside Car Down Onto Floorboards

My 2000 Camry has a sunroof with a wind shield on it. Back in April after I spent $1,600 on routine 90,000 maintenace, i.e. timing and all belts, new water pump, fuel injectors, etc., I began having water leak down onto the left floorboarad when it rains or I go though a car wash down onto the floorboards. The service department at the Toyota dealership has looked at it and tried to clean out/blowing out the left drain as they said it was probably stopped up. However, the problem has persisted and is now leaking on the passenger side. They have referred me to their body shop who wants $230 just to attempt to pinpoint the problem (removing headliner and side panels. Every one I’ve talked to about this situation has never heard of this. Do you have any ideas or suggestions as to what could be the problem?

The first idea was the one I would have suggested. However I would have noted that it is important to be careful when cleaning those drains as it is possible to damage one when cleaning it.

Note: In general dealers do an OK job, but they are not better or worse when it comes to maintenance. You can often get equal or better service at a local independent for far less money. That said, we have a Toyota in the family that usually goes to the dealer for service (most maintenance is done at home). The service department has proven to be very good. Too bad the sales department is not the same.