Preheat the oven to 350°F. Line two baking sheets with parchment paper.
Whisk flour, ginger, cinnamon, cloves, nutmeg, baking soda, baking powder, and salt in a large bowl.
Cream softened butter and brown sugar until light and fluffy, about 2–3 minutes.
Beat in molasses. Add eggs one at a time, then mix in vanilla until smooth.
Stir in dry ingredients in three additions, alternating with buttermilk in two. Mix just until combined. Rest batter 5 minutes.
Scoop 1½-tablespoon mounds onto sheets, spacing about 2 inches. Smooth peaks with a damp finger.
Bake 9–11 minutes, rotating pans halfway, until set and springy. Cool 5 minutes, then transfer to racks.
Make the filling: Beat cream cheese and butter until creamy. Gradually mix in powdered sugar, then vanilla, salt, cinnamon, and cream until fluffy.
Pair cookies by size. Pipe or spread about 1½ tablespoons filling on half the cookies; top with the rest and press gently.
Chill assembled whoopie pies 15 minutes to set the filling before serving.