Make Dough: Whisk dry ingredients. Cream butter and sugars. Beat in egg yolks and vanilla. Mix in dry ingredients just until combined. Scoop dough into 34 balls and create an indent with a 1/4 tsp measure.
Chill and Bake: Chill indented dough for at least 1 hour. Preheat oven to 350°F. Bake for 9–11 minutes. Immediately press indents again while hot. Cool completely.
Make Ganache: Heat heavy cream until just about boiling. Pour over chocolate chips and let sit for 1 minute. Stir until smooth.
Assemble: Fill each cookie well with about 1 tsp of ganache. Sprinkle with nonpareils, if desired. Chill in the fridge for 10-15 minutes to allow the ganache to set.
Notes
Texture: Using egg yolks helps ensure a rich, chewy cookie texture.
Shaping: Re-press the indents while the cookies are still hot, as they may shrink during baking.
Storage: Store leftovers in an airtight container for up to three days at room temperature.