Preheat your oven to 375°F (190°C) and line a 12-cup muffin tin with paper liners or grease it lightly.

In a medium bowl, whisk together the flour, baking soda, baking powder, salt, cinnamon, nutmeg, and ginger. Set aside.

In a large mixing bowl, combine 1 cup granulated sugar, brown sugar, canned pumpkin puree, eggs, vegetable oil, milk, and vanilla extract. Mix until smooth.

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

In a separate small bowl, beat the softened cream cheese, 1/4 cup granulated sugar, egg yolk, and 1/2 teaspoon vanilla extract until smooth and creamy.

Fill each muffin cup about 2/3 full with the pumpkin batter.

Add a small dollop (approximately 1 teaspoon) of the cream cheese mixture on top of each muffin. Use a toothpick or skewer to gently swirl the cream cheese into the batter.

Bake in the preheated oven for 18-22 minutes, or until a toothpick inserted into the center comes out clean.

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