Preheat the oven to 350 degrees F. Line 1 (12-cup) muffin pan with paper cupcake liners.
In a medium bowl, whisk together the flour, cocoa powder, baking soda, baking powder, and 1/4 teaspoon salt.
In a large bowl, beat the butter and the sugar together until light and fluffy.
Slowly beat in the eggs, 1 at a time. Mix together the milk, coffee, and vanilla in a measuring cup. Add 1/2 the dry ingredients to the butter mixture, beat to combine, then add the milk- coffee mixture and continue to beat, then add the remaining dry mixture. The mixture will look thick and airy.
Using an ice cream scoop, fill each cupcake liner 3/4 way full. Bake until a toothpick, inserted in the middle of the cupcake, comes out clean, about 20 minutes. Remove the cupcakes from the oven to a wire rack and let cool before frosting.
To make the frosting: Bring the heavy whipping cream to a gentle simmer. Add the chopped chocolate to a bowl with the butter and pour the hot cream over. Whisk the mixture until melted and smooth. Let it sit for 5 to 8 minutes until it thickens up.
Frost the cupcakes with the chocolate frosting using an offset spatula. Top each with a raspberry.