Preheat oven to 350 degrees Fahrenheit. Line baking sheets with a silicone baking mat or parchment paper. Set aside.
In the bowl of a stand mixer with the paddle attachment, cream the butter and both sugars. Add the eggs, and vanilla. Mix and scrape bowl.
In a separate bowl, whisk together the flour, cocoa powder, baking soda, and salt. Gradually add the dry ingredients to the wet ingredients, mixing until incorporated.
Set aside ½ cup of the chocolate chips, for topping the cookies. Add the rest of the chocolate chips to the mixing bowl. Mix gently on low speed until just combined, about 30 seconds.
Scoop cookie dough balls using a #30 scoop (about 2 Tbsp each) and place onto the prepared baking sheet about 3-inches apart. (8 cookies per tray.) Generously press chocolate chips into the tops of the cookie dough balls (about 5-6 per cookie) maintaining a round shape.
Bake at 350˚F for 10-11 minutes. For thicker cookies, press edges inward with a cookie spatula or swirl with a round cookie cutter while still warm. Sprinkle with flaky sea salt, if desired. Allow to cool for 1-2 minutes on the tray, then transfer to a wire rack to cool completely.
Notes
Use room temperature butter. This is colder than you think. The butter should be cold, and give a little when touched. Melted butter, or butter that is too soft, will make the cookies spread too thin. You can refrigerate the dough to help combat this.
For thick cookies: Shape the cookie dough balls tall and round. Press the edges of the cookies inward just after the tray comes out of the oven. I like to do this with a serving spatula or swirl around the cookies with a round cookie cutter. For the thickest cookies, refrigerate cookie dough balls for 30-60 minutes before baking.
FYI: This cookie dough is THICK. Use a stand mixer over an electric hand mixer when possible.
TO STORE: Store cookies in an airtight container at room temperature for up to 5 days.
TO FREEZE: Mix in all of the chocolate chips. Scoop cookie dough balls onto a parchment or silicone lined baking sheet. Set in the freezer for 1-2 hours until firm. Then transfer frozen dough balls into a freezer safe zip-top bag and freeze for up to 3 months. NOTE: You will need to bake cookies roughly 3-5 minutes longer, if baking from frozen.
TO FREEZE BAKED COOKIES: Freeze cookies in single layers divided by parchment paper, wrapped well or in a freezer bag, for up to 3-4 weeks. Thaw at room temperature.