Melt 1 stick butter in a small saucepan over medium-low heat and continue to cook until butter begins to smell nutty and lightly brown. Remove from heat and cool completely.
Place remaining stick of butter and cooled browned butter in a bowl and using an electric mixer, beat until light and fluffy.
Add both sugars and continue to beat together until light and fluffy.
Scrape down sides of the bowl, add molasses and vanilla and continue to mix together.
Stir in egg and egg yolk.
In another bowl whisk dry ingredients together and add to the butter mixture.
Beat together until a dough comes together.
Fold in chopped chocolate chips until fully combined.
Wrap dough in plastic wrap and chill in the refrigerator for at least 1 hour and up to 3 days.
Preheat oven to 350˚F.
Scoop 3 ½ tablespoon sized balls onto a parchment lined baking sheet, about 1 ½ inches apart and sprinkle with sea salt flakes.
Bake for 12 to 14 minutes or until cookies are golden brown.
Allow cookies to cool for 5 minutes before transferring to a cooling rack or serve warm.