Every single time she does this it reinforces the behavior, so she needs a setup where she can't perform the behavior while she is being trained out of it.
If it's to the extent where he's getting injured, but won't correct her and she's doing it so often I would separate them completely. We have a 5 month old pup and an adult dog in the house and use baby gates to limit the puppies access to the house and give the older dogs places to escape to that are puppy free.
When she is having supervised play time with the older dog, have her drag a leash so that you can pull her off when she starts getting too focused on that "part". If you can tell when she's thinking about it and interrupt her before she actually starts, that will help a lot to break the behavior.
Some other things you might try would be putting bitter apple or something else that tastes nasty on him to discourage her mouthing. Or you could get a belly band for him to wear while they are playing. She won't be able to get to him that way.