Preheat the oven to 350°F. Line a standard 12-cup muffin pan with paper liners.
Beat the softened cream cheese, granulated sugar, maple syrup, and vanilla until smooth. Set aside.
Whisk together the flour, baking powder, baking soda, cinnamon, ginger, nutmeg, and salt.
In a large bowl, whisk the pumpkin puree, eggs, maple syrup, brown sugar, melted butter, Greek yogurt, and vanilla until smooth. Fold in the dry ingredients just until no dry flour remains.
Divide the pumpkin batter among the 12 muffin cups. Spoon about 2 teaspoons of cream cheese mixture onto each muffin and make two or three loose swirls through the top.
Bake for 19 to 23 minutes, until the pumpkin portion springs back lightly and a tester inserted away from the cream cheese comes out without wet batter. Cool in the pan for about 10 minutes before moving to a rack.
Notes
Use pure pumpkin puree, not pumpkin pie filling. Swirl only the top portion so the cream cheese remains distinct.