Preheat oven to 425 degrees Fahrenheit and grease a muffin tin.
In a small bowl, combine brown sugar, cinnamon, melted butter, and a bit of flour to create a crumbly texture; set aside.
In a large bowl, whisk together the flour, baking powder, baking soda, salt, cinnamon, and pumpkin pie spice.
In a medium bowl, whisk together sugars, eggs, pumpkin puree, oil, milk, and vanilla extract.
Fold wet ingredients into the dry ingredients until just combined.
In a separate bowl, mix cream cheese, egg yolk, sugar, and vanilla until smooth.
Spoon one tablespoon of muffin batter into each liner.
Add a dollop of the cream cheese filling on top of the batter.
Fill the rest of the muffin cups with the remaining batter.
Top each with the prepared crumb topping.
Bake at 425 degrees for 5 minutes, then reduce heat to 350 degrees and bake for another 17 minutes until fully set.