Preheat your oven to 350°F (175°C) and line a muffin tin with paper liners.

In a large bowl, whisk together the all-purpose flour, whole wheat flour, baking powder, baking soda, salt, cinnamon, nutmeg, and ginger.

In another bowl, mix together the granulated sugar, brown sugar, pumpkin puree, vegetable oil, eggs, and 1 teaspoon of vanilla extract until well combined.

Gradually add the dry ingredients to the wet ingredients, stirring until just combined. Do not overmix.

In a separate bowl, beat the softened cream cheese with the powdered sugar and 1 teaspoon of vanilla extract until smooth and creamy.

Spoon about 2 tablespoons of muffin batter into each muffin cup, then add a dollop of the cream cheese mixture on top. Use a toothpick or knife to swirl the cream cheese into the muffin batter.

Top each muffin with additional muffin batter until the cups are about 3/4 full.

Bake in the preheated oven for 18-20 minutes, or until a toothpick inserted into the center comes out clean.

Allow the muffins to cool in the pan for 5 minutes, then transfer to a wire rack to cool completely.