Start by preheating your oven to 350ºF and lining your baking sheets with parchment paper.
In a medium bowl, whisk the flour, baking soda, baking powder, and salt together.
Melt the butter in a large microwave-safe bowl; then, vigorously mix in the peanut butter until smooth. Mix in both sugars, and then add the eggs and yolk one at a time, followed by the vanilla, mixing well after each addition.
Gradually incorporate the dry ingredients into the wet mixture until just combined, and then fold in the chocolate chips. If the dough is too crumbly, consider adding a splash of milk to reach the desired consistency.
If you have time, consider covering and refrigerating the dough for 24-72 hours to develop the flavors (allow it to soften at room temperature before baking).
If you'd prefer to bake immediately, scoop the dough into 3-tablespoon-sized balls onto the prepared baking sheets, and flatten each cookie slightly. Add a few extra chocolate chips on top for a bakery-style look.
Bake the cookies for 12 minutes until golden. Let them cool on the baking sheet for 5 minutes before transferring to a wire rack to cool completely.