In a medium bowl, whisk together the flours, baking soda, baking powder, and salt.
In the bowl of an electric mixer, beat the butter, granulated sugar, and brown sugar on medium-high speed until light and fluffy, about 2-3 minutes. Add the eggs and yolk, one at a time, beating well after each addition. Add the vanilla. Slowly beat in the flour mixture. Stir in the chocolate chips.
If time permits, wrap dough balls in plastic wrap and refrigerate for at least 24 hours but no more than 72 hours. This allows the dough to “marinate” and makes the cookies thicker, chewier, and more flavorful.
When ready to bake, place dough balls on prepared baking sheets, at least 2 inches apart.
Bake for 12-15 minutes, or until golden brown. Cool for 5 minutes before removing to wire racks to cool completely.
Although I prefer cookies fresh from the oven, these can be stored in an airtight container for up to 3 days. See pink tip box above the recipe for storage tips.