Preheat oven to 350 degrees F. Line a 9-inch x 9-inch baking dish with parchment paper, and then coat with non-stick cooking spray.
In a medium bowl, combine flour, baking powder, salt, ginger, cinnamon, nutmeg, clover, and pepper. Set aside.
In a large bowl, beat together butter and brown sugar for 1 to 2 minutes, until color lightens. Add molasses, eggs, and vanilla; mix to combine, scraping sides of bowl as needed.
Add half the dry ingredients to the wet ingredients, mix until just combined, Add the milk, and mix. Add the remaining dry ingredients, and mix until combined. Add chocolate chips and stir in with a spoon.
Transfer batter to the prepared baking dish, the batter will be thick. Spread evenly in the dish.
Bake for 45 to 55 minutes, until edges are browned and a toothpick inserted in the center comes out clean.
Remove from oven and cool completely on a wire rack.
Frosting:
In a medium bowl, beat together cream cheese, butter, and vanilla. Add powdered sugar and beat until smooth, 2 to 3 minutes.
Spread frosting evenly over the top of the cooled gingerbread.