Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners.
In a large bowl, whisk together the flour, baking soda, baking powder, cinnamon, nutmeg, ginger, and salt.
In another bowl, combine the granulated sugar, brown sugar, pumpkin puree, vegetable oil, eggs, and vanilla extract. Mix until well combined.
Gradually add the dry ingredients to the wet ingredients, stirring until just combined. Do not overmix.
In a separate bowl, beat together the softened cream cheese, powdered sugar, and vanilla extract until smooth.
Scoop about 2 tablespoons of muffin batter into each muffin cup. Add about 1 tablespoon of the cream cheese mixture on top of the batter, then cover with another tablespoon of muffin batter.
Bake for 20-25 minutes, or until a toothpick inserted into the center comes out clean.
Allow the muffins to cool in the pan for 5 minutes before transferring them to a wire rack to cool completely.