Preheat the oven to 350°F and line 12-15 cupcake tins with wrappers.
Measure the cocoa powder into a bowl and pour the boiling water over it. Use a fork to whisk the two ingredients together until they form a chocolate paste. Set this aside to cool. Then, in a separate bowl sift together the flour, baking soda, baking powder, and salt.
Grab a third, larger bowl, and whisk the eggs, oil, granulated sugar, and brown sugar together until smooth. Add the vanilla and cooled chocolate paste and continue whisking this mixture until it is smooth. Then add half of the flour mixture, followed by half the buttermilk, and then the remaining flour, gently folding ingredients each addition until just combined. Try to avoid over-mixing the batter. The batter should be runny.
Divide the batter evenly between the cupcake tins, filling until ¾ full and press a peanut butter cup into each cupcake. You'll get between 12-15 cupcakes. Bake for 19-22 minutes, or until the cupcakes are set. To test whether they're done, gently tap the cupcake tops. They should spring back instead of sink.
Pull the cupcakes out of the oven and let them cool in the pan for 5 minutes before transferring them to a wire rack to cool completely before frosting.