Preheat oven to 350ºF (180°C). Line baking sheets with parchment paper.
In a medium bowl whisk together the flour, baking soda, baking powder, and salt.
In a large heat safe bowl, microwave the butter until melted. Vigorously stir in the peanut butter into the hot butter until well combined. Stir in the granulated sugar and brown sugar until well combined. Add the eggs and yolk, one at a time, stirring well after each addition. Add in the vanilla. Gradually stir in the flour mixture. Cut the chocolate into pieces and add to the dough.
Divide the dough into balls using a spring-loaded scoop and drop onto prepared baking sheets. Flatten dough slightly into disc shapes with your palms.
Bake for 12-15 minutes, or until golden brown. Let cool for 5 minutes before removing to wire racks to cool completely. Cookies can be stored in an airtight container at room temperature for up to 3 days.