Preheat oven to 400 degrees. Line a muffin tin with paper liners then spray muffin tin and liners with non stick cooking spray. In a small bowl, beat cream cheese, sugar and vanilla extract and set aside.
In a large bowl, combine pumpkin, eggs, brown sugar, milk, honey, vegetable oil, pumpkin pie spice, vanilla extract, baking powder, baking soda and salt. Stir in flour just until combined.
Divide pumpkin batter evenly between muffin cups. Use a standard size ice cream scoop or a 1/4 cup measuring cup to portion batter. Then spoon heaping tablespoon of cream cheese mixture unto muffins and use a toothpick to swirl the batter.
Bake for 20 minutes or until toothpick inserted into edge of muffins, not cream cheese mixture, comes out clean.