Preheat the oven to 350°F.  

Heat the butter in a small saucepan until it turns an amber color and smells nutty. For a deeper flavored cookie, we let it get dark brown. Transfer the brown butter to a small heatproof bowl and set aside to cool to room temperature, about 15 minutes. 

Meanwhile, mix together the flour, baking soda and salt in a medium bowl. In a large bowl, mix together the brown sugar and granulated sugar with the cooled brown butter until well incorporated and slightly fluffy. Add the vanilla and mix. Add the eggs and mix until the mixture is fluffy and turns a lighter brown color. 

Pour the dry ingredients into the wet ones and mix until just incorporated. Don’t overmix—flour streaks are okay. Add the dark chocolate and chocolate chips and mix JUST until they are incorporated. Let the dough sit, covered, at room temperature or in the fridge, for at least 30 minutes. It can also be stored in the fridge overnight.  

Spoon the dough onto baking sheets, leaving adequate space in between. We usually portion out 3 tablespoons per cookie, which yields 10 to 12, but you can make them any size you like. Bake until golden brown around the edges with slightly underbaked centers, about 10 to 12 minutes, assuming they are about 3 tablespoons each. If you prefer a crisper cookie, bake them longer. 

Once the cookies are out of the oven, top each one with 2 to 3 dark chocolate chunks and let melt (about 2 minutes). Generously sprinkle the cookies with sea salt and let sit for about 20 minutes before serving. This will allow the cookie to firm up, yet still be warm, resulting in a crunchy exterior and chewy, soft interior.  

Note: To fully stop the baking process and firm up the cookies faster, after salting the tops, carefully transfer them with a spatula to a clean baking sheet or platter and freeze for 10 minutes. Let sit at room temperature for 5 minutes, then enjoy!