Preheat oven to 350 degrees F. Liberally grease a 24-cavity miniature muffin pan with cooking spray. Place one ball of cookie dough into each muffin cup. Using your fingers, gently press it into the cup.
Bake the cookie cups for approx. 8-10 minutes or until golden brown, slightly crisp edges and the centers look just about set. Do not over bake. Cool in the pan for about 10 minutes.
After they've briefly cooled, use the handle of a wooden spoon to make indentations in the center of each cookie cup, careful not to puncture all the way through. Allow the cookie cups to cool completely, then gently pop them out of the muffin tin and place on a wire rack.
In a large bowl, combine the chocolate chips and heavy cream. Microwave on HIGH power for about 25 seconds. Stir, then microwave again for another 20 seconds. Stir until smooth and glossy.
Evenly distribute the chocolate ganache into each cookie cup. Sprinkle with sea salt. Serve immediately, or let set.