Try Oxy Clean.....dilute it with water for stain removal (ratio on package), put it in a squirt bottle, spray the items and let them sit for 30 minutes. Then take a soft bristle brush (the soft rubber brushes made for carpet cleaning work best, or you could use an old toothbrush), scrub the moldy areas, then rinse and try to get excess water out of items by applying pressure to a towel wrapped over/around the item....oxy clean is great for upholstery, I used it to get black mold spots off of some deck chairs that were left out over the winter. I have never been able to get those black mold spots out of anything once they appear....I was really impressed that I now have an option to clean that stuff rather than have to just throw the item away.
You can buy leather and suede cleaner and then use baking soda after the cleaning or even better if you have some of the little bags of silicone that come with packages. Put this inside of the shoe and it will absorb the moisture and keep the shoes dry. Use a shoe tree after the cleaning, you know the things that you put inside of the shoe to retain the shape. If you don't have any use news paper after cleaning and stuff it inside of the shoe with either the baking soda or silicone bags while the shoes dry after cleaning.