Preheat oven to 350 F. Line a 12 cup cupcake pan with cupcake liners. In a large bowl, whisk together flour, sugar, baking powder, baking soda, salt, cinnamon, ginger and nutmeg.
Add in eggs, milk, vegetable oil, molasses and vanilla extract, whisk until smooth. Evenly divide cupcake batter between the lined cupcake pan. Bake for 18-20 minutes. Let cool completely.
For the cream cheese frosting, in a large bowl using either a hand or stand mixer, beat softened cream cheese with softened butter until fluffy. Add in powdered sugar, milk and vanilla extract and beat until smooth. Pipe or spread frosting onto cupcakes.
