Preheat your oven to 350°F. Get 4 baking sheets ready by lining them with parchment paper.
In a medium bowl, combine the flour, pumpkin pie spice, salt, baking powder, and baking soda, then set it aside.
In a larger bowl, whisk the pumpkin purée, both sugars, melted butter, eggs, and 1 teaspoon of vanilla extract until everything is well blended.
Slowly fold the dry mixture into the wet ingredients, stirring just until combined. Drop spoonfuls of batter (about 2.5-3 tablespoons each) onto the baking sheets, keeping them spaced 2 inches apart.
Bake for 12-15 minutes or until a toothpick comes out clean from the center of the cookies. Let them rest on the baking sheet for 10 minutes before transferring them to a cooling rack.
While the cookies cool, whip the softened butter and cream cheese together for 3-4 minutes until smooth. Gradually add in the powdered sugar, mixing until well incorporated. Add the heavy cream and vanilla, beating on high for another 2-3 minutes until the filling is fluffy and creamy.
After the cookies are fully cooled, flip half of them upside down and spread or pipe a generous amount of filling on the flat side. Top with the remaining cookies and gently press down to form sandwiches.
Chill the assembled whoopie pies in the refrigerator for at least 30 minutes before serving to set the filling.