To make the cupcakes, preheat the oven to 350°F. Line two 12-cup cupcake pans with cupcake liners. Set aside.
In a large bowl, whisk together the flour, sugar, cocoa powder, baking powder, baking soda, and salt.
Heat the milk to a simmer in a small pot over medium heat. Turn off the heat and stir in the peanut butter, half of the chocolate chips, vinegar, and vanilla. Stir until everything is smooth. When the chocolate chips are completely melted, pour the milk mixture into the bowl with the flour mixture. Stir to combine. Fold in the remaining ½ cup of chocolate chips. Fill the cupcake liners 2/3 of the way full with batter. Bake for 18 to 22 minutes, or until a toothpick inserted in the center comes out clean. Allow to cool completely before frosting.
To make the chocolate ganache, use a small pot to bring the coconut milk to a simmer. Remove the pot from the heat and add the chocolate. Swirl the pot around so that the chocolate is covered by the milk. Cover and let sit for several minutes until the chocolate melts. Remove cover and stir until glossy and smooth. Let the ganache cool slightly before frosting the cupcakes. The longer the ganache sits, the thicker it will get. Use a spoon to swirl the ganache on the cupcakes or position the cupcakes on a wire cooling rack with a baking tray underneath. Drizzle ganache over the cupcakes. Cool slightly before serving. Cupcakes stay fresh at room temperature in an airtight container for several days or store covered in the refrigerator for up to 1 week.