Preheat your oven to 350°F. Line two 12-cup muffin pans with 18 paper liners.
In a large bowl, mix the pumpkin puree, granulated sugar, brown sugar, oil, eggs, and vanilla until everything is smooth and well combined.
1 cup pumpkin puree, 3/4 cup granulated sugar, 1/2 cup brown sugar, 1/2 cup vegetable oil, 2 large eggs, 1 teaspoon vanilla extract
In a medium bowl, whisk together the remaining dry ingredients for the muffins. (Take care not to use the streusel ingredients here.)
1-3/4 cups all-purpose flour, 1 teaspoon baking soda, 1/2 teaspoon baking powder, 1/2 teaspoon salt, 2 teaspoons pumpkin pie spice, 1 teaspoon ground cinnamon
Add the dry ingredients to the pumpkin mixture a little at a time. Stir just until combined. Be careful not to overmix the batter.
To make the cream cheese filling, beat the cream cheese, sugar, egg yolk, vanilla, and flour together until smooth and creamy.
8 ounces cream cheese, 1 large egg yolk, 1 teaspoon vanilla extract, 2 tablespoons all-purpose flour, 1/3 cup granulated sugar
Fill each muffin cup about halfway with pumpkin batter. Spoon a little of the cream cheese mixture into the center of each muffin.
Mix the streusel ingredients together until crumbly, then sprinkle it generously over the tops of the muffins.
2 tablespoons brown sugar, 1/2 teaspoon cinnamon, pinch salt, 2 tablespoons melted butter, 1/4 cup all-purpose flour
Bake for 20 to 22 minutes, until the muffins are set and a toothpick inserted into the pumpkin portion comes out clean.
Let the muffins cool in the pan for about 5 minutes, then transfer them to a wire rack to finish cooling.
Store leftover muffins in the refrigerator for up to 5 days. For the best texture, let them come to room temperature before serving.