Preheat the oven to 350º.
Line a baking sheet with parchment paper.
Whisk together the flour, baking soda, baking powder, cinnamon, ginger, nutmeg, and salt and set aside.
In a separate bowl, beat together the butter and both sugars until light.
Add the eggs and the vanilla and beat until combined.
Stir in carrots.
Mix in the flour mixture just until combined.
Using a medium cookie scoop, drop about 2 tablespoons of dough onto the prepared baking sheet, spacing them 2 inches apart.
Bake for 15-20 minutes each or until they begin to brown.
Remove from the oven. Allow to cool completely before filling.
FOR THE FILLING: Beat together the cream cheese, butter, and vanilla until combined.
Slowly mix in the powdered sugar, and beat until smooth.
To assemble the whoopie pies, spread or pipe the filling onto the flat side of one cake. Top it with another cake, flat-side down. Repeat with the rest of the cakes and filling.