In a small bowl, beat together the softened cream cheese, sugar, and vanilla extract until smooth and creamy. Transfer the mixture to a piping bag or a plastic zip-top bag with the tip cut off. Set aside.
Preheat your oven to 350°F (175°C). Line a 12-cup muffin tin with paper liners or spray with non-stick cooking spray.
In a large bowl, whisk together the flour, granulated sugar, brown sugar, baking powder, baking soda, salt, cinnamon, nutmeg, cloves, and ginger.
In a separate bowl, whisk together the eggs, pumpkin puree, vegetable oil, milk, and vanilla extract until well combined.
Gradually add the wet ingredients to the dry ingredients, stirring just until combined. Be careful not to overmix, as this can make the muffins dense.
Fill each muffin cup with batter, filling about 3/4 of the way.
Pipe a small amount of the cream cheese filling into the center of each muffin. Gently push the tip into the batter to ensure the cream cheese goes into the middle, leaving a small dollop visible on top. Add pepitas if using.
Bake the muffins in the preheated oven for 18-22 minutes, or until a toothpick inserted into the muffin (not the cream cheese center) comes out clean.
Allow the muffins to cool in the pan for 5 minutes before transferring them to a wire rack to cool completely.
These muffins are best served slightly warm. Store any leftovers in an airtight container in the refrigerator for up to 5 days.