Preheat the oven to 350° and position 2 racks in the lower and middle third of the oven.
Line 24 muffin cups with paper or foil liners.
Put the cocoa powder in a medium heatproof bowl.
Add the boiling water and whisk until a smooth paste forms.
Whisk in the buttermilk until combined.
In a medium bowl, sift the flour with the baking soda, baking powder and salt.
In a large bowl, using an electric mixer, beat 1 1/2 sticks of the butter with the granulated sugar until light and fluffy, about 3 minutes.
Beat in the eggs and vanilla, then beat in the dry ingredients in 2 batches, alternating with the cocoa mixture.
Carefully spoon the cupcake batter into the lined muffin cups, filling them about two-thirds full.
Bake for 20 to 22 minutes, or until the cupcakes are springy.
Let the cupcakes cool in the pans for 5 minutes, then transfer them to wire racks to cool completely.
In a medium bowl, beat the peanut butter with the remaining 3 tablespoons of butter until creamy.
Sift the confectioners' sugar into the bowl and beat until light and fluffy, about 2 minutes.
Spoon all but 3 tablespoons of the peanut butter filling into a pastry bag fitted with a 1/4-inch star tip.
Holding a cupcake in your hand, plunge the tip into the top of the cake, pushing it about 3/4 inch deep.
Gently squeeze the pastry bag to fill the cupcake, withdrawing it slowly as you squeeze; you will feel the cupcake expand slightly as you fill it.
Scrape any filling from the top of the cupcake and repeat until all of the cupcakes are filled.
In a small saucepan, bring the heavy cream to a simmer.
Off the heat, add the semisweet chocolate to the cream and let stand for 5 minutes, then whisk the melted chocolate into the cream until smooth.
Let the chocolate icing stand until slightly cooled and thickened, about 15 minutes.
Dip the tops of the cupcakes into the icing, letting the excess drip back into the pan.
Transfer the cupcakes to racks and let stand for 5 minutes.
Dip the tops of the cupcakes again and transfer them to racks. Spoon the remaining 3 tablespoons of peanut butter filling into the pastry bag and pipe tiny rosettes on the tops of the cupcakes.
MAKE AHEAD The cupcakes are best served the same day they are made, but they can be refrigerated overnight in an airtight container.
If you don't have a pastry bag with a fitted tip, you can fill these cupcakes by carving a hole in the center (from the top) with a sharp paring knife. Put the filling in a resealable plastic bag and snip off one of the corners. Pipe the filling directly into the hole.