Add the flour, baking soda, baking powder, and sea salt to a small bowl and whisk to combine.
Add the butter and sugar to a large bowl and beat on high until fluffy. Then add the peanut butter, eggs, and vanilla and beat until fully combined.
Add the flour to the peanut butter mixture 1/2 cup at a time until fully incorporated, then cover and refrigerate for at least two hours and up to two days.
Preheat the oven to 350 F and line a baking sheet with parchment paper.
Roll the dough into one-inch balls and place on a baking sheet two inches apart. If filling with chocolate, make a deep indent in each ball with your thumb. Bake for 10-12 minutes, until browned and crisp on the outside.
Remove the cookies from the oven and immediately either fill with melted chocolate, or press a miniature peanut butter cup into each cookie. Let cool until chocolate is set, then enjoy!