Stone foundations can be a challenge to waterproof. Many would think that excavating around the outside of a stone foundation and applying a waterproofing membrane would be the best way to repair it. However care needs to be taken when removing soil from around an old stone foundation. Many contractors chose NOT to excavate such afoundation but rather make sure all external grading is pitch away from the stone foundation. Making sure to divert all downspouts at less 10 feet away.
Re-pointing the stone foundation maybe a good idea especially if the mortar between the stone is loose and brittle. Sometimes it is necessary to install a basement waterproofing system under the basement slab. When installing a basement drainage system care is needed to make sure not to disturb the stone foundation , nor remove any soil that is within the zone of influence.
It is recommended that you hire a reputable basement waterproofing contractor to look at your stone foundation and make recommendations as to waterproofing it or at least help you control the water and keep it out of your basement.