Preheat oven to 350F degrees. Line two muffin pans with cupcake liners. Set aside.
In a large bowl, mix the flour, baking powder, baking soda, and salt together until combined. In a medium microwave-safe bowl, melt the butter. Whisk in the granulated and brown sugars. Mixture will be thick. Vigorously whisk the egg, yogurt, milk, vanilla, and lemon zest until combined and uniform in texture. Slowly whisk the wet ingredients into the dry ingredients until no lumps remain. Gently fold in the blueberries.
Divide batter among 14 cupcake liners and bake in batches for 20 minutes or until a toothpick inserted in the center comes out clean. Allow to cool.
While the cupcakes cool, beat the cream cheese and butter together on medium speed until smooth, about 2 minutes. Add the confectioners' sugar and 1 Tbsp cream. Beat for 2 minutes. Add the vanilla and 1 more Tbsp cream if needed to thin out. Beat for 1 minute. Taste the frosting and add a pinch of salt if too sweet. Frost cooled cupcakes immediately before serving.
Unfrosted cupcakes remain fresh covered tightly at room temperature for 3 days. Store frosted cupcakes in the refrigerator for up to 2 days and allow to come to room temperature before serving.