Preheat oven to 375°F (190°C). Line a muffin pan with paper liners or spray with non-stick spray.
Cream Cheese Filling: In a medium bowl, beat cream cheese until smooth. Add sugar, egg yolk, and vanilla. Mix until creamy and thick. Set aside.
Muffin Batter: In a large bowl, whisk together flour, granulated sugar, brown sugar, baking powder, baking soda, cinnamon, and salt. In a separate bowl, mix melted butter, eggs, sour cream, and vanilla. Pour wet mixture into dry and mix until just combined.
Streusel Topping: In a small bowl, combine brown sugar, flour, and cinnamon. Cut in cold butter with a fork until mixture resembles coarse crumbs.
Assemble: Fill muffin cups 1/3 full with batter. Add 1 tbsp cream cheese mixture in the center of each. Cover with more batter, then top generously with streusel.
Bake for 18–22 minutes or until a toothpick inserted in the muffin part comes out clean. Let cool in pan for 5 minutes, then transfer to wire rack.