Had same problem with Mk2 and current MK4.
Cheapest route, pull off old seal, clean out the groove, and then fill groove with silicone, and ease back onto the boot lip.
The water getting in generally enters about where the boot latch is, but in fact appears to get up into the seal somewhere near the top of the boot, which is why you really need to take the whole strip out and clean it.
I clean out the cr*ppy old mastic with a cloth and blunted flat head screwdriver (means you do not damage the seal when cleaning).
Takes about 60 to 90 mins, and saves a fortune.