Place 8 ounces cream cheese in the bowl of a stand mixer (or large bowl if using an electric hand mixer). Let sit at room temperature until softened, about 30 minutes. Meanwhile, arrange a rack in the middle of the oven and heat to 350°F. Line a standard 12-well muffin pan with paper liners.
Add 1 teaspoon of the vanilla extract to the cream cheese. Beat with the paddle attachment on medium speed until fluffy, about 1 minute. Scrape down the sides of the bowl and the beater with a rubber spatula. Add 1/3 cup of the granulated sugar, 1 of the large eggs, and 1/4 teaspoon kosher salt. Beat on low speed until combined and mostly smooth (a few lumps are okay), about 1 minute more. Add 1/2 cup mini chocolate chips and beat on low speed until just combined.
Bring 1/2 cup water to a simmer in a small saucepan over medium heat. As soon as the water comes to a simmer, turn the heat off. (Alternatively, use an electric or stovetop tea kettle and bring it to a boil.)
Place 3/4 cup all-purpose flour, the remaining 3/4 cup granulated sugar, 1/2 cup unsweetened cocoa powder, 3/4 teaspoon baking powder, 3/4 teaspoon baking soda, and the remaining 1/2 teaspoon kosher salt in a medium bowl. Whisk to combine.
Add the remaining 1 large egg, 1/2 cup milk, 1/4 cup canola or vegetable oil, 2 teaspoons apple cider or white vinegar, and 1 teaspoon vanilla extract. Whisk to combine. Pour in the hot water and whisk to combine. The batter will be quite thin.
Divide the batter evenly between the wells in the pan, filling each no more than 3/4 full. Dollop each with 2 tablespoons of the cream cheese mixture, dividing it evenly among the cupcakes.
Bake until a toothpick inserted in the center of the cupcakes comes out clean, about 25 minutes. Let the cupcakes cool in the pan for about 10 minutes, then transfer to a wire rack to cool completely.