increasing the strength of the muscles used to crush the stone, the strength bones and ligaments that the bones are pulling against and the strength of the joints is a start but you also need a surface area that is harder than the stone to apply the force to.
so imagine a plate like armour around the fingers and hands, like scales, which are composed of a substance harder than the stones you are trying to crush but not too brittle (diamond?). then its simply a matter of increasing the strength of the muscles to the point in which the stone crumbles under their force and a skeletal structure that resists the forces better than the stones. eventually there would be a limit and like SZCZERZO KŁY points out it is important what stone your crushing as he would have more trouble crushing diamonds than sandstone.
without increasing the size of the hands your left with changing their material and density. so your looking at applying the latest advancement's in material science to their bodies (carbon fiber bones?).
edit: a quick experiment you can carry out is to get a couple of coins between finger and thumb and try to crush something in between them, I bet you will be surprised by what you can crush.