Preheat your oven to 375°F (190°C). Line a standard 12-cup muffin tin with paper liners or lightly grease the cups with nonstick spray.

In a large mixing bowl, whisk together the flour, granulated sugar, brown sugar, baking soda, baking powder, salt, cinnamon, nutmeg, ginger, and cloves.

In another bowl, whisk the eggs, pumpkin puree, vegetable oil, milk, and vanilla extract until smooth.

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

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

Spoon the pumpkin batter into the muffin cups, filling each about 2/3 full.

Add a heaping teaspoon of the cream cheese filling to the center of each muffin. Use a toothpick or skewer to gently swirl the cream cheese into the batter, if desired.

Sprinkle the tops of the muffins with raw or coarse sugar for a crunchy topping, if using.

Bake the muffins in the preheated oven for 18-22 minutes, or until a toothpick inserted into the center (avoiding the cream cheese) comes out clean.

Let the muffins cool in the pan for 5 minutes before transferring them to a wire rack to cool completely.