Whisk together flour, cocoa powder, salt, and baking powder in a bowl. Cream butter, brown sugar, and granulated sugar in a separate bowl for 2 minutes. Beat in egg yolks and vanilla until combined.

Gradually add the flour mixture to the wet ingredients, mixing until just combined. Use a cookie scoop to form 1 tablespoon-sized balls and indent centers with a measuring spoon.

Preheat oven to 350°F (175°C). Bake cookies for 9 to 11 minutes. Gently press indents again if needed after baking.

Heat cream until boiling. Pour over chocolate chips, let sit for 1 minute, then stir until smooth to make ganache.

Fill each cookie's indent with ganache and sprinkle with nonpareils if desired. Chill cookies in the refrigerator until ganache sets.