Hubbie's grandmother used to disinfect her kids' stuffed animals by spraying Lysol liberally over them, then tossing them in the dryer on high heat.
That would be the first thing I would do.
If that doesn't work, I'd suspect the mildew was coming from the inner stuffing, and I'd discard the toy.
If its possible to open the toy at a seam, pull out the old stuffing and replace it with new stuffing, that could work. I would only do this if the toy has sentimental meaning.