In a mixing bowl, whisk together flour, cocoa powder, baking powder, baking soda and salt for 30 seconds, set aside. In the bowl of an electric stand mixer fitted with the paddle attachment, whip butter, granulated sugar and brown sugar on medium-high speed until pale and fluffy, about 3 - 4 minutes. Add in eggs one at a time, mixing until combined after each addition and adding vanilla in with second egg. With mixer set on low speed, slowly add in dry ingredients and mix just until combined. Stir in chocolate chips. Transfer to an airtight container and refrigerate 2 hours.
Meanwhile, line a baking sheet with wax paper and dollop 1 1/2 tsp of Nutella at a time onto lined baking sheet into individual little mounds, repeat until you have made 30. Transfer to freezer and freeze 1 hour.
Preheat oven to 350 degrees. To assemble and bake cookies, remove dough from refrigerator and scoop dough out about 2 Tbsp at a time and shape into balls. Remove about 4 nutella dollops from the freezer at a time (so the Nutella doesn't soften at room temperature, you want it to stay firm as it's much easier to work with this way) and using your thumbs make an indentation in the center of the dough ball, large enough to fit a Nutella dollop (so it should look similar to a bowl). Take frozen Nutella and place it in the center of the indentation, then wrap and press cookie dough around Nutella to cover entirely (so the Nutella doesn't seep out while baking). Transfer prepared cookie dough balls to a Silpat lined (or buttered) baking sheet and bake in preheated oven 9 - 12 minutes. Remove from oven and sprinkle tops lightly with sea salt if desired. Allow to cool several minutes on baking sheet before transferring to a wire rack to cool. Store in an airtight container.
*For a more richly chocolate cookie you can increase the cocoa powder up to an additional 1/4 cup, then reduce the flour by that same amount (so if you add 2 additional Tbsp cocoa reduce the flour by 2 Tbsp).
** I set aside some of the chocolate chips to press into the tops of the cookies just before baking, probably about 1/2 cup, because I like to have some of the chocolate chips showing. It's optional, if you don't care to have some of the chocolate chips showing then just mix all of them inches.