Preheat oven to 350°F and line baking sheets with parchment paper.
In a medium bowl, whisk together flour, cocoa powder, baking soda, and salt.
In a large bowl, beat butter and both sugars until light and fluffy, about 3 minutes.
Add eggs and vanilla to butter mixture and beat until well combined.
Gradually stir the dry ingredients into the wet ingredients until just combined.
Fold in the dark chocolate chunks until evenly distributed throughout the dough.
Drop rounded tablespoons of dough onto prepared baking sheets, spacing them 2 inches apart.
Bake for 10-12 minutes until edges are set but centers still look slightly underdone.
Remove from oven and immediately sprinkle with flaky sea salt.
Let cool on baking sheet for 5 minutes before transferring to a wire rack.