Preheat the oven to 350°F (175°C). Line a muffin tin with cupcake liners.
In a large mixing bowl, sift together the flour, cocoa powder, granulated sugar, baking powder, baking soda, and salt.
Add the milk, vegetable oil, egg, and vanilla extract to the dry ingredients and beat on medium speed for 2 minutes.
Stir in the boiling water until the batter is well combined. The batter will be thin.
Fill each cupcake liner about two-thirds full with batter.
Bake for 18-20 minutes, or until a toothpick inserted into the center of a cupcake comes out clean.
Remove from the oven and allow the cupcakes to cool in the pan for 5 minutes before transferring them to a wire rack to cool completely.
To make the cream filling, beat the softened butter in a medium mixing bowl until smooth.
Gradually add the powdered sugar and vanilla extract, beating until smooth and creamy.
Add the heavy cream and beat on medium-high speed for 2 minutes, until light and fluffy. Transfer the filling to a piping bag fitted with a round tip.
Once the cupcakes are completely cooled, insert the tip of the piping bag into the center of each cupcake and gently squeeze to fill with cream.
To make the chocolate ganache, place the chocolate chips in a heatproof bowl.
In a small saucepan, heat the heavy cream and butter over medium heat until it begins to simmer. Pour the hot cream mixture over the chocolate chips and let sit for 2-3 minutes.
Whisk the chocolate and cream until smooth and glossy.
Let the ganache cool slightly before spooning it over the filled cupcakes. Allow the ganache to set before serving.