Preheat oven to 350 degrees F. Line muffin tins with paper liners. Set aside.
In the bowl of a stand mixer, stir together sugar, flour, cocoa, baking powder, baking soda and salt.
Add eggs, milk, oil and vanilla. Beat on medium speed for one minute or until batter is smooth. Slowly pour in boiling water and mix until batter is smooth. Don't over mix.
Fill liners about 1/2 full with batter. Bake cupcakes for 18-22 minutes or until a toothpick inserted in the center comes out clean. Remove from oven and cool completely on wire rack before frosting.
While the cupcakes are cooling, make the frosting. In the bowl of stand mixer, beat the butter on medium speed until light and fluffy, about 2-3 minutes. Gradually add the powdered sugar and mix until the frosting is smooth, about 3-4 minutes. Mix in the vanilla. Drizzle in the cooled melted chocolate and beat on medium speed until the frosting is smooth and creamy.
To make the chocolate ganache, add the chocolate chips to a medium bowl. Heat the cream in a small saucepan over medium heat just until it bubbles around the edges or you can heat it in the microwave. Pour cream over the chocolate chips. Let the mixture stand for 30 seconds, then stir until the chocolate melts and a smooth ganache comes together, about 1-2 minutes.
Place the frosting in a pastry bag. Spoon the ganache onto the center of the cupcake. Spread to the edge of the cupcake. Let the cupcakes sit until the ganache firms up, about 5 minutes. Pipe chocolate buttercream frosting over the ganache. Decorate with mini chocolate chips, if desired.
Note-if you want to pipe a high frosting swirl on the cupcakes, you might need to double the frosting recipe. It just depends on how high you go with the frosting.