In a small bowl, mix all of the ingredients together. Cover and freeze until chilled, about 30 minutes.
In a bowl, combine the flour, brown sugar, cinnamon and salt. Work in the butter with your fingers. Press the mixture into small clumps. Refrigerate the topping until chilled, about 15 minutes.
Preheat the oven to 350° and line a 12-cup muffin tin with paper or foil liners. In a medium bowl, whisk the flour with the cinnamon, nutmeg, cloves, baking soda, baking powder and salt. In a large bowl, using an electric mixer, beat the eggs with the brown sugar, oil and pumpkin puree. Beat in the dry ingredients until evenly incorporated.
Spoon half of the batter into the prepared muffin cups. Drop heaping teaspoons of the cream cheese filling in the center of each cup and spoon the remaining batter on top. Sprinkle the crumb topping over the batter. Bake for about 30 minutes, until a toothpick inserted in the center of the muffins comes out clean. Let the muffins cool for 10 minutes before turning them out onto a rack to cool completely.
The muffins can be stored in an airtight container at room temperature for up to 3 days.