Preheat the oven to 350ºF. In a medium bowl, stir together the flour, baking powder, baking soda, salt, and pumpkin pie spice.
In a separate large bowl, whisk together the eggs, granulated sugar, brown sugar, pumpkin purée, oil, and vanilla extract.
Pour the bowl of dry ingredients into the bowl of wet ingredients and stir together just until combined. A few small lumps are okay, just try not to overmix.
In a separate small bowl, stir together the cream cheese and sugar for the cream cheese filling.
Grease a muffin tin or line with muffin liners. Fill each well in the muffin pan about ⅓ full. Add a small dollop of the cream cheese to each well, in the center of the muffin batter. Divide the remaining muffin batter between each well, covering the cream cheese. Each well in the muffin pan should be filled about ¾ full.
Bake the muffins for about 24 minutes, or until fully puffed in the center and slightly cracked on top.
Remove the muffins from the oven and let them cool for about 5 minutes before gently removing them from the muffin pan and allowing them to finish cooling on a wire rack.