Preheat oven to 350 degrees. Prepare a standard, 12 cup muffin tin by lightly greasing or lining with paper liners.
In a small bowl stir together the flour, baking powder, baking soda and all the spices and salt. Set aside.
In a larger bowl beat together the soft butter and sugar until fluffy. Add in the eggs, one at a time until combined. Add the vanilla and pumpkin and mix well.
Add the dry ingredients to the wet, mixing just until combined, then folding in the chocolate chips. Add one large spoonful to the bottom of each muffin cup. Add one piece of cream cheese to each cup and press down slightly. Top with the remaining batter and place in the oven. Bake at 350 degrees for 20-22 minutes until a toothpick inserted into the middle of a muffin comes out clean. Remove from the oven and let muffins cool in the tin for about 5 minutes before removing and placing on a cooling rack to finish cooling.