Preheat oven to 350 degrees. Line 2 large baking sheets with parchment paper.

In a medium sized mixing bowl, combine the flour, baking soda, baking powder, and salt. Set aside.

In a large bowl or the bowl of an electric mixer, beat together the butter and peanut butter until light and fluffy. Add both sugars and beat until smooth. Add the egg and beat until completely combined. Beat in the milk and vanilla extract.

With the mixer on low speed, slowly add the flour mixture to the peanut butter mixture. Once it's mostly combined, turn the mixer up to medium speed and beat until cohesive.

Scoop rounded Tablespoons of dough onto the prepared baking sheets. Bake for 6 minutes. Remove from oven. Use the back of a spoon to create thumbprint indents in the center of each cookie. Fill with 6-8 chocolate chips. Return to oven and bake for an additional 4-6 minutes or until barely set.

When the cookies come out of the oven, swirl chocolate chips with a toothpick or chop stick until they form a pool of chocolate goodness. Sprinkle with sea salt. Allow to set up on the baking sheet for a few minutes then remove and cool completely.