Line two baking sheets with parchment paper and set aside.

In a medium-sized bowl, whisk together the flour, baking soda, baking powder, and salt. Set aside.

In the bowl of a stand mixer, beat together the butter and peanut butter for a minute or so. Add the sugars and cream together for about 2 minutes, or until light and fluffy, scraping down the sides of the bowl as needed.

Add the vanilla extract and eggs, one at a time. Make sure the first egg is incorporated before adding the second.

In a couple of batches, add the dry ingredients to the wet. Scrape down the sides of the bowl as needed.  Fold in the dark chocolate.

Using a cookie scoop, drop the dough onto the prepared cookie sheets. Chill for 30 minutes (or up to 2 days).

Preheat the oven to 350 degrees F.  With the refrigerated dough balls a few inches apart from one another, bake for 12-14 minutes, or until the edges are golden brown. Sprinkle the warm cookies with sea salt.

Allow the cookies to cool on the cookie sheet for about 5 minutes before removing them to a wire rack to cool completely.