Preheat the oven to 375°F (190°C) and line a 12-cup muffin pan with paper liners or lightly grease the cups.
In a small bowl, beat together the softened cream cheese, sugar, and vanilla until smooth. Set aside.
In a large bowl, whisk together the flour, baking powder, and salt.
In another bowl, whisk together the granulated sugar, brown sugar, eggs, melted butter, milk, and vanilla extract.
Pour the wet ingredients into the dry ingredients and stir until just combined. Do not overmix.
Gently fold in the blueberries.
Fill each muffin cup about halfway with batter. Add about 1 tablespoon of the cream cheese mixture to the center of each muffin, then cover with additional batter until each cup is about ¾ full.
Sprinkle the tops with coarse sugar and lemon zest if desired.
Bake for 20–25 minutes, or until the tops are lightly golden and a toothpick inserted into the muffin (avoiding the cream cheese center) comes out clean.
Cool in the pan for 5 minutes, then transfer the muffins to a wire rack to cool completely.