Another option, assuming you can have a small amount of downtime, is to simply to shut down the VM, unpresent (do NOT delete) the virtual disks, then clone. After you have one clone, re-add the disks (in the correct order of SCSI target ID) then you are all set.
OR - if you want to get into the weeds of things, put a snapshot on the VM, then via command line, use vmkfstools to make a copy of the boot disk.