Preheat the oven to 350 degrees F. Line two muffin pans with 14 paper liners.
For the cupcakes, in a large bowl, combine 1-2/3 cups flour, baking powder, baking soda and salt. In a medium bowl combine the butter and both sugars. Whisk in the yogurt, milk, vanilla extract, lemon zest and egg. Fold the wet ingredients into the dry ingredients.
In a small bowl, toss the blueberries in the remaining flour before gently stirring into the batter. Transfer to the prepared muffin pan. Bake for 20 minutes until a tooth pick inserted into the center of the cake comes out clean. Allow the cupcakes to cool completely before removing from the pan.
For the frosting, using an electric mixer, beat the cream cheese and butter on medium speed until combined, about 2 minutes. Add the sugar, milk and vanilla extract, beating until smooth, about 3 minutes.
Once the cupcakes have cooled, use a pastry bag fitted with a round tip to pipe the frosting or spread it with a spatula. Top with fresh blueberries.
Store the cupcakes in the refrigerator up to 2 days.