In the bowl of a stand mixer, cream together the butter and sugars until light and fluffy, about 2 minutes.
Add the egg, egg yolk, and extracts and mix until well incorporated.
In a bowl, whisk together the flour, baking soda, baking powder, and salt. Add half of the flour mixture to the butter mixture. Mix until just combined. Add the remaining flour and mix until just combined. Fold in the chocolate.
Using a two tablespoon cookie scoop, portion the dough out onto a parchment-lined baking sheets. Press extra chips into the top of the dough. Chill for 30-45 minutes, or overnight.
Preheat oven to 350 degrees.
Bake cookies for 9-11 minutes. The middle of the cookies will look slightly underdone, but they will set up as they cool. Sprinkle with flaky salt, if desired. Allow the cookies to cool on the baking sheet for three minutes before transferring to a cooling rack.
Store in an airtight container for 3-4 days.
To freeze cookie dough: With a cookie scoop, portion the dough out onto a parchment-lined baking sheet and freeze until firm, about 30 minutes. Then, transfer the dough to a zipper-top freezer bag. Store for up to 3 months. To bake: Place the frozen dough on a parchment-lined baking sheet and bake as directed in the recipe, allowing for a few extra minutes of bake time.
To freeze cookies: Allow the cookies to cool completely. Transfer to a zipper-top freezer-safe bag and store for up to one month. To serve, thaw the cookies at room temperature.