Preheat oven to 350°F. Line two baking sheets with parchment paper or silicone baking mats. If not using mats, spray the cookie sheets with cooking spray.
In the bowl of a stand mixer fitted with the paddle attachment, or using hand beaters, beat the butter and brown sugar on medium speed for 2 minutes or until fluffy. Add the molasses and mix until combined. Add the eggs, one at a time, mixing well after each addition.
Add the baking soda, ginger, cinnamon, salt, and cloves and flour. Mix until combined.
Scoop the soft dough into 24 - 1 ¾" inch balls. Roll each ball in granulated or coarse sugar. Place the balls on the baking sheet about 2 inches apart from one another.
Bake for 9-11 minutes or until the edges are set and lightly golden brown. Cool the cookies on the cookie sheet for 2-3 minutes and then transfer the cookies to a cooling rack to cool completely.
Cream Cheese Filling
In a medium bowl beat the cream cheese until smooth. Add the powdered sugar and vanilla and beat until smooth.
Assemble the Whoopie Pies
To make the whoopie pies spread or pipe the filling on the flat sides of half of the cookies. Gently Press the flat sides of the remaining cookies against the filling. Chill the whoopie pies to help the filling set. Store in the fridge for 2-3 days.