there are two different ways to control ownership of ntfs and msdosfs filesystems. The hard way is to specify the user and group when mounting the filesystem - use the -u and -g options: check man
mount_msdosfs(8)
The easy way, and better, is to set the user, group and permissions of the mount point. Unmount the filesystem, set the mount point's owner and permissions, and remount the filesystem. All files in the filesystem will now have the same permissions as the mount point. (executable permissions excetped: -x on directories will be carried over, but will be cleared on regular files)
I do not know of any way to remap these uids when mounting filesystems. It is an option you can specify when exporting a filesystem over NFS. (which, of course, is no help whatsoever!) Man pages did not help me either, there.