Preheat oven to 350℉. Line a baking sheet with parchment paper.
Begin by browning the butter. Place the butter in a small sauce pot and bring up to a simmer. Cook for about 10 minutes or until little brown bits form on the bottom of the pan and it smells nutty. The butter will foam up twice and after the 2nd time the milk solids will start to brown.
Set aside and let cool.
In a medium bowl combine the flour, baking soda, baking powder and sea salt together. Whisk together.
In a stand mixer fitted with a paddle attachment add both sugars and the cooled brown butter. Mix together for a few minutes. It will look like it’s separating but it’ll come together once you add the eggs. Add in the eggs and vanilla, mixing thoroughly between egg additions.
Next add in the flour mixture and mix until you no longer see any flour bits. Stir in the chocolate chunks by hand.
Using a medium ice cream or portion scoop, scoop cookies onto baking sheet, 2-inches apart. Gently flatten cookies with the palm of your hand; sprinkle with flaky salt.
Bake 9 to 10 minutes; let cookies cool slightly before transferring them to a cooling rack. Repeat with remaining dough.