Preheat oven to 350°F (180°C). Line baking sheets with parchment paper.

In a medium heatproof bowl, combine peanut butter, chopped chocolate, and butter. Place bowl over a saucepan of simmering water, and heat, stirring occasionally, until melted and well combined. Remove from heat, and let cool for 15 minutes.

In a medium bowl, whisk together flour, cocoa, baking powder, baking soda, and kosher salt.

In the bowl of a stand mixer fitted with the whisk attachment, beat eggs at medium speed until frothy. Add confectioners’ sugar, brown sugar, and vanilla, and beat at low speed until combined. Increase mixer speed to high, and beat until mixture is thick and fluffy, 4 to 5 minutes. Switch to the paddle attachment; add peanut butter mixture and flour mixture, and beat at low speed until well combined, stopping to scrape bottom and sides of bowl.

Using a 3-tablespoon spring-loaded scoop, scoop dough (about 53 grams each), and roll into balls. (Dough will be soft but should not stick to your hands.) Place 3 inches apart on prepared pans.

Bake until edges are set and tops look dry and crinkled, 10 to 13 minutes, rotating pans halfway through baking. Gently press several chocolate chips into top of each hot cookie, and sprinkle sea salt on top. Let cool completely on pans on wire racks. Store in an airtight container for up to 3 days.