Have you tried a slightly abrasive cleaner like Vim? (It is a general purpose cream/paste cleanser, a little bit like toothpaste with Comet mixed in). I find if it can't get something off a pony (or anything vinyl, really), then nothing will (It'll get things even the magic eraser can't touch sometimes). Of course, as it is slightly abrasive, it is not good to use it on a ponies symbol or eyes (I haven't had any problems, but... I wouldn't recommend it), but I find their porous vinyl isn't hurt by it, and it's certainly better than mold!
I've been using it for years and never wrecked a pony with it (it has not affected their aging either), but as with any new cleaning product and a vintage toy, you should be careful with it if you choose to try some, and test it under a hoof or other inconspicuous area. Also, it will take the "patina" off the vinyl, for lack of a better word. The build up of oils from being handled and stuff that non-porous cleaners often miss. So, the vinyl can look a little duller after using it (magic eraser does this too sometimes).