Get 16 ounces of cream cheese into a stand mixer bowl and let it chill for 30 minutes. Preheat the oven to 350 degrees and line your muffin pan with paper liners.
Add 2 teaspoons of vanilla extract to cream cheese and beat until fluffy. Mix in ½ teaspoon kosher salt, two large eggs, and ⅔ cup of granulated sugar until smooth. Add a cup of mini chocolate chips.
Simmer 1 cup of water in a saucepan or use a tea kettle for boiling.
In a medium bowl, whisk together 1 ½ cups granulated sugar, 1 ½ cups all-purpose flour, 1 cup unsweetened cocoa powder, 1 ½ teaspoons baking soda, 1 ½ teaspoons baking powder, and the remaining kosher salt.
Mix the last two large eggs, 1 cup milk, ½ cup vegetable or canola oil, 4 teaspoons white vinegar or apple cider, and 2 teaspoons vanilla extract into the dry ingredients. Whisk until smooth. Pour in hot water and whisk again.
Divide the batter evenly, making sure not to exceed ¾ full in each well. Spoon 4 tablespoons of the cream cheese mixture onto each cupcake.
Bake at 350 degrees for about 25 minutes or until the inserted toothpick comes out spotless. Cool in the pan for 10 minutes, then transfer the cakes to a wire rack.