Preheat oven to 350°F; line baking sheets with parchment.
Whisk flour, cocoa, baking soda, and salt in a medium bowl.
Beat butter and both sugars in a large bowl about 3 minutes, until light and fluffy.
Beat in eggs and vanilla well.
Gradually stir dry ingredients into wet just until combined.
Fold in dark chocolate chunks evenly.
Drop rounded tablespoons onto prepared sheets, 2 inches apart.
Bake 10-12 minutes, until edges set and centers look slightly underdone.
Immediately sprinkle with flaky salt.
Cool on sheet 5 minutes; transfer to wire rack.