Cant remove windows partition from mac(not BOOTCAMP)
I just had a similar issue and solved it by following @VDR's answer but it required slight modifications.

Open Terminal and run

$diskutil list


diskutil will return something similar to 

/dev/disk0    

:                       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


/dev/disk1...

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
Unmounting disk
Erasing
Initialized /dev/rdisk0s3 as a 29 GB HFS Plus volume with a 8192k journal
Mounting disk
Finished erase on disk0s3 old_win


Your empty volume will now be manageable from the graphical Disk Utility app.