Brown the butter. Add butter to a small saucepan over medium heat. Stir constantly until the butter melts, foams, and begins to turn amber with brown flecks on the bottom of the pan and a nutty aroma. This takes about 12 minutes — don't rush it. Remove from heat immediately once you see small brown flecks forming.
Transfer the browned butter to a room-temperature bowl to stop it from cooking further. Allow to cool for about 15 minutes.
In a large bowl, whisk together the flour, baking soda, baking powder, salt, and cinnamon. Set aside.
In a separate large bowl, combine the cooled browned butter, brown sugar, granulated sugar, eggs, and vanilla extract. Mix until well combined.
Slowly add the flour mixture to the butter-sugar mixture and stir until just combined.
Check the dough. If it still feels warm, allow it to cool slightly before adding in the chocolate. Gently fold in the chocolate chunks or chips.
Using your hands, shape the dough into balls about 2 inches wide. The dough will be slightly greasy from the browned butter - totally normal. For flatter cookies, gently press each ball with the back of a measuring cup. Place the cookie dough balls on a plate or baking sheet, cover with plastic wrap, and refrigerate for at least 1 hour, or overnight.
When ready to bake, preheat the oven to 350°F. Arrange chilled dough balls on a parchment-lined baking sheet, spacing them at least 2 inches apart. Sprinkle with flakey sea salt if desired.
Bake for 14-16 minutes. The cookies will look slightly underdone, which is what you want. They will finish setting as they cool on the pan.
Allow cookies to rest on the baking sheet for 5-10 minutes before transferring to a wire rack.
Notes
Don't rush the butter browning. It took about 12 minutes; yours may vary depending on the type of butter and pan you use. Look for the butter to turn a golden amber color and for the brown bits to start appearing to know it's done.
Cool the browned butter slightly before adding to the sugars.
Check dough temperature before adding chocolate. If it's warm, the chunks will melt before baking.
Chill time is non-negotiable. One hour minimum; overnight produces a better cookie.
Cookies will look underbaked at 14-16 minutes. Pull them anyway — they finish on the hot pan.
To freeze: shape into balls, freeze solid on a baking sheet, then transfer to a bag. Bake from frozen at 350°F for 16-18 minutes.