Preheat the oven to 375°F (190°C) and line a 12-cup muffin pan with paper liners.
Beat the softened cream cheese, 1/4 cup granulated sugar, egg yolk, and 1/2 teaspoon vanilla until smooth. Set aside.
To make the streusel, combine 1/2 cup flour, 1/3 cup brown sugar, and 1 teaspoon cinnamon. Stir in the melted butter with a fork until irregular crumbs form.
In a large bowl, whisk together 1 3/4 cups flour, baking soda, baking powder, 2 teaspoons cinnamon, pumpkin pie spice, and salt.
In another bowl, whisk the pumpkin puree, 1/2 cup brown sugar, 1/2 cup granulated sugar, eggs, vegetable oil, and 1 teaspoon vanilla until smooth.
Pour the wet ingredients into the dry ingredients and fold gently until just combined.
Fill each muffin cup approximately one-third full with pumpkin batter.
Place approximately 1 tablespoon cream cheese filling into the center of each muffin.
Cover with additional pumpkin batter until the cups are nearly full.
Sprinkle the cinnamon streusel over each muffin.
Bake for 18–22 minutes, until a toothpick inserted into the pumpkin portion comes out clean or with a few moist crumbs.
Cool in the muffin pan for 10 minutes.
Transfer to a wire rack and allow to cool further before serving.