Make the Cookie Dough: Add the semi sweet chocolate chips, bittersweet chocolates, and butter to a large microwave safe bowl and microwave in 30 second intervals, stirring between each, until fully melted and smooth. The mixture will be super thick! Let cool for a few minutes. Add the eggs and sugar, and mix with an electric mixer on high speed for 4 minutes. This will give the cookies the structure they need, and a nice crinkly top. Add the vanilla and give a quick mix. Add the flour, cocoa, baking soda, and salt and mix until everything is combined. It will seem too wet to be cookie dough here, and that's just right. Stir in the peanut butter chips and chocolate chunks.
Chill the Dough & Shape Balls: Cover the bowl with a clean kitchen towel and chill for 30 minutes in the freezer or 1 hour in the fridge. The dough will now be stiff enough to scoop into balls. Form seven, 6-ounce (170 g) balls of dough. Press extra peanut butter chips and chocolate chunks onto the tops of the dough balls.Place the balls into an airtight container or onto a lined baking sheet covered with the towel and chill for 2 more hours in the fridge (for a total of 3 hours), or up to 2 days in the fridge.
Bake: Preheat oven to 325° F. Line a couple of baking sheets with parchment paper or a silicone baking mat. Bake 3 cookies per cookie sheet. Bake for 14-16 minutes. The edges will appear and feel just set. Let cool about 20-30 minutes before digging in.
Serve + Store: These are best while warm & gooey, with a sprinkle of flaky sea salt and a cold glass of milk! Store leftovers in an airtight container at room temp for about a week. Re-warm cookies gently in the oven or microwave to regain that gooey-ness.
Freezing the Dough: The cookie dough can be frozen in an airtight container for up to 2 months. Let dough balls thaw in the fridge overnight before baking as usual.