Preheat oven to 375 degrees F. Place paper baking cups into muffin pan, lightly spray with nonstick cooking spray and set aside.
In a medium bowl, whisk together flour, pumpkin spice, baking soda, and salt. In a separate, larger bowl, whisk together the pumpkin puree and sugar. With pumpkin and sugar combined, beat in the eggs, vegetable oil and vanilla extract until fully combined. Carefully whisk in the flour mixture until there are no lumps. Fill muffin cups until they are approximately 3/4 full.
In a medium bowl beat the cream cheese until soft and smooth. Add the sugar, egg yolk and vanilla extract and beat again until fully combined.
Top each muffin with approximately 1 tablespoon of cream cheese frosting (depending on how full your muffin cups are, you may have a little leftover cream cheese mixture). Using a toothpick, carefully swirl the cream cheese with the pumpkin batter. Don't worry if it looks a bit messy, it will bake up much prettier.
Bake for approximately 18 minutes or until toothpick inserted in the center comes out clean. Remove from oven and allow to cool before serving.