Line a standard 12-cup muffin pan with paper liners. Preheat the oven to 425°F.
Make the filling. Beat the cream cheese and granulated sugar until smooth. Mix in the egg yolk and vanilla just until combined. Refrigerate while making the batter.
Make the streusel. Stir the flour, brown sugar, cinnamon, and salt together. Add the melted butter and toss with a fork until crumbs form. Set aside.
Whisk the flour, baking soda, baking powder, cinnamon, ginger, nutmeg, cloves, and salt in a medium bowl.
In a large bowl, whisk the pumpkin, brown sugar, granulated sugar, eggs, oil, milk, and vanilla until smooth.
Fold the dry ingredients into the pumpkin mixture just until combined. Do not overmix.
Add about 1 1/2 tablespoons of batter to each muffin liner. Spoon a heaping tablespoon of cream cheese filling into the center of each. Cover with the remaining pumpkin batter.
Divide the streusel evenly over the tops and press it down very lightly.
Bake at 425°F for 5 minutes. Keep the oven door closed, reduce the temperature to 350°F, and bake for 15 to 18 minutes more.
Check the pumpkin portion with a toothpick. It should come out clean or with a few moist crumbs. Cool in the pan for 10 minutes, then transfer the muffins to a wire rack for at least 20 minutes.
Store cooled muffins in an airtight container in the refrigerator for up to four days.