Is there a Linux tool for defragging NTFS partitions?

There is a universal tool that can do defragmentation on linux called shake. You can download the source, or for Ubuntu users there's a PPA (the shake package in the official repository is unrelated).

I've just tested it on an NTFS filesystem mounted using ntfs-3g and it seemed to work without problems (no errors, the verbose output looks typical). So probably is filesystem-independent... Almost, since it can make use of extended attributes. To work without making use of those, you should use the -X option. Try using

shake --old=0 -v -X /some/directory/

From my experience, it has to be run as root.