Begin by browning the butter. Place the butter in a small sauce pot and bring up to a simmer. Cook for 10-15 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 slightly.
In a medium bowl combine the flour, baking soda, baking powder and sea salt together. Mix to incorporate. Set aside.
In a stand mixer fitted with a paddle attachment add both sugars and the slightly 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 just until you no longer see any flour bits. Stir in the chocolate chunks by hand.
Using a medium sized cookie scoop, scoop the batter onto a parchment or silicone lined baking sheet. Gently flatten the cookies with your hand so they are no longer mounded. Sprinkle with the flaky sea salt.
Bake for 10-12 minutes or until golden brown around the edges but still soft in the middle. Remove and let cool fully on a cooling rack.