Heat the oven to 375°F (190°C). Line a standard 12-cup muffin pan with paper liners.
Combine the flour, brown sugar, cinnamon, and salt in a medium bowl. Stir in the melted butter until moist crumbs form. Refrigerate while preparing the remaining components.
Beat the softened cream cheese and sugar until smooth. Beat in the egg yolk and vanilla, scraping the bowl as needed. Set aside.
In a medium bowl, whisk the flour, baking soda, baking powder, cinnamon, ginger, nutmeg, cloves, and salt.
In a large bowl, whisk the pumpkin, eggs, oil, brown sugar, granulated sugar, milk, and vanilla until smooth and glossy.
Fold the dry ingredients into the pumpkin mixture just until no dry streaks remain. Do not overmix.
Divide about half of the pumpkin batter among the liners. Place a rounded teaspoon of cream cheese filling in the center of each, keeping it away from the sides. Cover with the remaining batter and top evenly with the chilled streusel.
Bake for 20 to 24 minutes, until a toothpick inserted into the pumpkin portion comes out with a few moist crumbs. Cool in the pan for 10 minutes, then move the muffins to a wire rack for at least 20 minutes before serving.