I just had a similar issue and solved it by following @VDR's answer but it required slight modifications.
Open Terminal and run
diskutil will return something similar to
: TYPE NAME SIZE IDENTIFIER
0: GUID_partition_scheme *128.0 GB disk0
1: EFI 209.7 MB disk0s1
2: Apple_HFS MountainLion 64.0 GB disk0s2
3: Microsoft Basic Data 31.8 GB disk0s3
4: 21686148-6449-6E6F-744E-656564454649 1.0 MB disk0s4
5: 0FC63DAF-8483-4772-8E79-3D69D8477DE4 14.7 GB disk0s5
6: Linux Swap 17.2 GB disk0s6
The NTFS volume I want removed is at 3, run
$diskutil **eraseVolume** JHFS+ old_win /dev/disk0s3
You'll see output similar to...
Started erase on disk0s3
Initialized /dev/rdisk0s3 as a 29 GB HFS Plus volume with a 8192k journal
Finished erase on disk0s3 old_win
Your empty volume will now be manageable from the graphical Disk Utility app.