Preheat the oven to 350°F. Set a rack in the middle of the oven. Butter a 10-inch cast iron skillet and set aside.
Sift whole wheat flour, baking powder, baking soda and sea salt into a medium bowl.
In the bowl of a stand mixer fitted with the paddle attachment, add the butter, dark brown sugar and white sugar. Mix on low until the butter and sugars are well combined (about 2 minutes). Scrape down the sides, then add an egg. Mix until combined, then repeat with other egg. Mix in the vanilla. Add the flour mixture to the bowl in two additions, mixing on low speed until the flour is just combined. Don't overmix here!
Scrape down the sides and add 3/4 of the chocolate chunks, mixing just until the chocolate is evenly incorporated. Scrape the batter into the prepared skillet, pressing it out into an even layer. Sprinkle remaining chocolate across the top, and gently press into the dough.
Bake the cookie until deep golden brown along the edge (35 - 45 minutes). The center should be set and an inserted toothpick will come out clean. Remove from oven and let cool a bit before serving.