Preheat oven to 350°F. Line 12 muffin tins with liners and set aside.
In the bowl of your mixer, combine sugar, flour, baking soda, baking powder, and cocoa powder.
Add eggs, milk, oil and mint extract and beat on medium speed for 2 minutes.
Slowly stir in boiling water. Fill muffin tins evenly with batter and bake for about 20 minutes or until tops spring back when lightly touched in the center.
Let cool completely on a wire rack.
In the bowl of your mixer, beat butter, cream cheese, milk and mint extract on medium speed until smooth.
With the mixer on low, slowly add powdered sugar, beating until just combined. Increase speed to medium high and beat for one minute.
Frost cooled cupcakes using a spatula, or a piping bag fitted with a large round piping tip.
Place cupcakes in the refrigerator to let the frosting chill for 30 minutes prior to dipping in the coating.
In a microwave safe bowl, heat chocolate chips and shortening, stopping every 30 seconds to stir until combined and smooth.
Remove cupcakes from the refrigerator and hold upside down, dipping each in the chocolate mixture.
Let the excess chocolate drip off for a moment before placing back on your plate and topping with a Junior Mint.