In a medium bowl, whisk together the all-purpose flour, baking soda, and salt. Set aside.

In a large mixing bowl, using an electric mixer on medium speed, beat the softened unsalted butter, packed light brown sugar, and granulated sugar until light and fluffy, about 2-3 minutes. Scrape down the sides of the bowl as needed.

Beat in the large eggs one at a time, mixing well after each addition. Stir in the pure vanilla extract until just combined.

Gradually add the whisked dry ingredients to the wet ingredients, mixing on low speed until just combined. Be careful not to overmix; stop as soon as no dry streaks of flour remain.

Fold in the semi-sweet chocolate chips and milk chocolate chunks (if using) with a rubber spatula until evenly distributed.

Cover the bowl with plastic wrap and refrigerate the dough for at least 30 minutes, or up to 24 hours. Chilling is highly recommended for best results as it prevents spreading and deepens flavor.

Preheat your oven to 375°F (190°C). Line two baking sheets with parchment paper.

Scoop rounded tablespoons (or use a 1.5-inch cookie scoop) of chilled dough onto the prepared baking sheets, leaving about 2 inches between each cookie. If desired, press a few extra chocolate chips onto the tops of the dough balls for a prettier finish. Sprinkle lightly with flaky sea salt.

Bake one sheet at a time for 9-12 minutes, or until the edges are golden brown and the centers are still slightly soft and puffy. The exact baking time will depend on your oven and desired chewiness. For chewier cookies, bake closer to 9-10 minutes. For crispier edges, bake closer to 11-12 minutes.

Let the cookies cool on the baking sheets for 5 minutes before transferring them to a wire rack to cool completely. This helps them set and prevents breaking.