The way the radiologist explained it to me was that MS lesions are close to fluid and blood spaces and PML lesions are usually found in white matter NOT adjacent to those vessels and spaces. He also said MS lesions are usually oval in shape and PML lesions are irregularly shaped in most cases, and most of them do not enhance with gadolinium, but that is not always the case.
There are lots of images of PML lesions out there and the ones I have seen are scary, like the Blob eating a brain...