Preheat your oven to 350°F (175°C).
In a large bowl, whisk together the dry ingredients: flour, baking soda, ginger, cinnamon, cloves, and salt.
In another bowl, beat the softened butter and brown sugar until light and fluffy, about 2-3 minutes.
Add the egg, molasses, and vanilla extract to the butter mixture, mixing until combined.
Gradually add the dry ingredients to the wet ingredients, mixing until just combined.
Drop rounded tablespoons of dough onto a lined baking sheet, spacing them about 2 inches apart.
Bake for 10-12 minutes or until the edges are set and the tops are slightly cracked.
Remove from the oven and let cool on the baking sheet for 5 minutes before transferring to a wire rack to cool completely.
While the cookies cool, prepare the cream cheese filling by beating together the softened cream cheese, powdered sugar, and vanilla extract until smooth.
Once cookies are completely cooled, spread a generous dollop of filling on the flat side of half the cookies and top with the remaining cookies, flat side down.
Refrigerate the assembled whoopie pies for about 30 minutes to set the filling before serving.