$6k for a clutch and the IMS sounds like a rip off. Must be some sort of NYC tax.
Keep shopping.
Parts cost should be the same no matter where you go and the rest is labor. My indie charged me 8 hours labor at $85/hour to do the IMS and RMS. Clutch is already out so that should not add much in terms of labor. I got the LN single row bearing at $650 plus the RMS seal which was so little in cost I don't even remember.
I'd say anything more then $3k is too much.