I have a 1901 home in northern Maine and would like to get some input on the best way I could insulate a stone foundation. I have many cracks between the rocks and cold air from the outside frozen ground is causing a cold draft into the basement. I am considering spray foam but would like some tips and best locations of material to get this method done. Or is there another idea I should consider.

You cannot foam the walls and leave it exposed as it when becomes a fire hazard. Foam must be covered.

You can build frame walls and insulate them.
The cracks are not the cause of the drafts. If they are the cracks are really big.
You could re-point them to seal them up. But if the basement is not used for anything other then storage, insulate the floor above and let the basement breath. That air flow can help prevent mold growth and poor indoor air quality.