I'm not aware of any publicly available Linux tool that supports this. It's in the plans for ntfsck
from ntfsprogs, the most advanced publicly available package for NTFS (see ntfsprogs\ntfsck.c
in its source), but that's about it. (You might be able to contract the developers to implement this for you. This isn't so hard technically, just time and effort.)
So, your best bet for now is to boot from a Windows live media (MS DaRT is the official one for repair tasks) and run chkdsk /r
.
I also succeeded in booting from a Linux Live CD, sharing the block device with Samba, then mounting and checking it over the network from a Windows machine with ImDisk.
Alternatively, How to unmark an NTFS cluster as bad? outlines how to do this by hand. Basically, it's editing NTFS metadata in a hex editor.