Preheat oven to 350F. Line 36 muffin tins with paper liners. Set aside.
In a medium bowl, combine the flour, baking soda, and salt. Set aside.
In a small bowl, add the chocolate chips and butter. Microwave on medium power for 1 1/2-2 minutes, or until chocolate chips are melted, stirring halfway through. Once melted, stir thoroughly to remove any lumps. Set aside.
In a large bowl, add sugar and melted chocolate. Beat with an electric hand mixer or stand mixer with fitted paddle attachment until combined. Add eggs one at a time, beating well after each addition, followed by vanilla extract.
Beat in flour mixture until smooth, alternating with milk. Spoon mixture 2/3 full into each muffin tin.
Bake for 20-22 minutes, or until toothpick inserted into center of cupcake comes out clean. Remove from oven and let cool completely.
To make the frosting, add butter and peanut butter to a large bowl. Cream for 3 minutes until light and fluffy.
Add powdered sugar, 1/2 cup at a time, beating well after each addition. Add heavy cream and vanilla extract, stirring to combine.
Pipe or spread onto cooled cupcakes and top with a mini peanut butter cup, if desired.