Preheat oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners.
In a bowl, whisk together flour, baking powder, baking soda, salt, and spices.
In another bowl, whisk sugars, eggs, oil, pumpkin, milk, and vanilla until smooth.
Add dry ingredients to wet and stir until just combined.
Divide batter evenly among cupcake liners.
Bake for 18–20 minutes or until a toothpick comes out clean.
Let cool in the pan for 5 minutes, then transfer to a rack to cool completely.
For frosting, beat cream cheese and butter until smooth.
Add powdered sugar and vanilla, and beat until creamy.
Pipe or spread frosting onto cooled cupcakes.