In large pot, cook squirrels by boiling in water to cover until tender. Remove from cooking broth, reserving broth; when squirrels are cool enough to handle, pull meat from bones.
In mixing bowl, combine flour, egg, milk, salt and pepper. Work into a small ball. On lightly floured board, roll dough out 1/8 inch thick, cut into 3 inch squares.
Heat reserved broth to boiling. Drop dough, squirrel meat, potatoes, and onion into boiling broth, adding in layers until everything is in pot. Cover pot and cook for 20 to 30 minutes, or until potatoes are tender and dough is cooked.