Whisk flour, baking powder, and baking soda in a medium-sized bowl.
Beat butter and sugar in a large bowl until light and fluffy, about three minutes using an electric or stand mixer.
Beat in eggs, yogurt, vanilla, and milk until blended.
Alternately fold in flour mixture and melted chocolate, beginning and ending with the flour mixture.
Fill cupcake liners 2/3 full.
In a small bowl, mix cream cheese, sugar, and egg until smooth.
Stir in chocolate chips.
Spoon one heaping tablespoon of the topping on top of the batter in each cupcake liner.
Bake at 350 F for 25 minutes or until a toothpick comes out clean.
The easiest way to melt the chocolate is the microwave in 20 second bursts. Stir between each burst until the chocolate is completely melted.If needed, you can substitute sour cream for the yogurt.You can also replace the dark chocolate in the cupcakes and topping with semi-sweet chocolate if you prefer.