The bearing in my a/c clutch is noisy and feels a little rough, found out when I was changing the timing belt at 172k. The cheapest I have seen the clutch is $500 at 1stvwparts. The local stealership told me $750 which made me laugh quite hard.
Changing the clutch requires the $80 VAG 1719 tool and it may or may not go well and you will still have an old compressor. Basically the tool is a clutch puller and once the old one is off you have to drive the new one on, if it then has too much or too little gap then you need to remove it again, shim it and try again. I found searching for 'vag 1719 compressor' got me some good links to the clutch servicing directions, like this one
http://serial.cc/pdfs/AC_COMPRESSOR_SERVICING.pdfPlan B for me is to buy a complete unit from ECS for $348, take the car to a shop and have the a/c sucked dry, swap the a/c and drier myself then go and have it refilled.
Venting R134A in to the atmosphere or refilling a system you repaired is illegal.
Sorry, different year and all that, so ymmv. I wasn't looking for a 99 so no guarantees on the prices and such. Good luck.