TO MAKE THE MUFFINS: Preheat the oven to 375 degrees F. In a medium bowl, whisk together the flour, baking soda, baking powder, salt, sugar, brown sugar, pumpkin pie spice and cinnamon. Set aside.
In a large bowl, whisk together the pumpkin puree, melted butter, vegetable oil, vanilla extract, egg and milk. Whisk until the pumpkin mixture is smooth- be sure not to overmix.
Stir in the dry ingredients into the wet ingredients in 1/3 increments at a time. Mix with a wooden spoon until combined and the batter should be smooth. Set aside.
TO MAKE THE CREAM CHEESE SWIRL: With an electric mixer, mix together the softened cream cheese, egg yolk, vanilla extract and sugar in a small bowl for 3-4 minutes or until light and fluffy. The cream cheese mixture will resemble a frosting.
CINNAMON SUGAR TOPPING: In another small dish combine the cinnamon and sugar and mix with a spoon.
ASSEMBLE THE MUFFINS: Line a muffin pan with cupcake liners and use a standard ice cream scoop to scoop out the pumpkin muffin mixture into each muffin cup. If you don't have an ice cream scoop, simply fill each muffin cup 3/4 full. This batter makes 12-14 muffins.
ADD CREAM CHEESE SWIRL: Spoon about 1 tablespoon of the cream cheese filling into the center of each muffin. Top off each muffin until you run out of cream cheese swirl filling. Use a toothpick or knife to carefully swirl the cream cheese with the pumpkin batter. Don't mix the cream cheese in completely, a few swirls is perfect! Top each muffin with a pinch of the cinnamon sugar mixture.
Bake the muffins for 15-17 minutes until the tops are set. Remove from the muffins from the muffin pan once they are slightly cooled and place on a cooling rack. Once cooled, enjoy!