Preheat oven to 350 F. Line a 12 cup muffin pan with cupcake liners. In a measuring cup, combine milk and vinegar. Let sit for 5 minutes. In a large bowl, whisk together flour, sugar, cocoa powder, salt, baking powder and baking soda.
Add milk mixture, eggs and vegetable oil into the dry ingredients. Whisk until smooth. Evenly divide cupcake batter between 12 lined muffin tins. Bake for 20-25 minutes. Let cool completely.
For the cream cheese frosting, in a large bowl using either a hand or a stand mixer, beat softened butter and cream cheese together until creamy. Add in powdered sugar, vanilla extract and milk as needed until desired consistency. Pipe frosting onto cooled cupcakes.
