Preheat your oven to 375 and line your muffin tin with liners.
In a medium bowl stir together the flour, spices, soda, salt. Once combined add the pumpkin and stir. Then add in the sugars, the eggs, oil and extract. Stir until blended.
Fill your muffin tins 3/4th full.
In a new bowl, beat the cream cheese until smooth. Mix well with the sugar, egg and extract. Once smooth drop a big dollop on top of each muffin. Use a butter knife to dip the cream cheese mixture into the pumpkin mixture. Just a quick swirl.
Bake 20-25 minutes or under a toothpick inserted in the center comes out clean.
I used a whisk for the muffin and a pastry blender to mix the cream cheese swirl.