In a medium saucepan, melt the butter over medium heat, then bring it to a boil. Once it starts boiling, stir the pan constantly until the butter becomes a deep amber color. It's hard to see through the foam, but get a spoon and scoop some up to check the color. Remove from the heat, pour into a separate bowl (this allows the butter to stop cooking) and allow the butter to cool for 20 minutes.
While the butter is cooling, preheat the oven to 350 degrees and line a baking sheet with parchment paper.
In a large bowl, whisk together the flour, baking soda, and sea salt. Set aside.
Add the brown sugar, granulated sugar, eggs, and vanilla to the cooled butter and stir to combine. Pour the flour mixture into the bowl with the sugar and egg mixture. Stir using a wooden spoon until the dough comes together and the ingredients are evenly incorporated. Stir in the chocolate chunks.
Using a medium (2-tablespoon) cookie scoop, drop the dough 2 inches apart on the baking sheet. Bake for 10 to 12 minutes, until edges are lightly golden.
Allow the cookies to cool for 5 minutes on the baking sheet, then transfer them to a wire rack to cool completely. If desired, sprinkle a small amount of flaked sea salt on top of the cookies as they are cooling.
Store airtight at room temperature for up to 3 days or freeze for up to three months.