Adjust oven rack to lower-middle position and preheat oven to 400 degrees F. Line two standard muffin pans with cupcake liners.
Make the Cheesecake Filling: In a medium bowl, beat the cream cheese, sugar and salt on medium speed until smooth, about 30 seconds. Beat in the egg whites and sour cream until combined, about 1 minute. Stir in the chocolate chips using a rubber spatula; set aside.
Make the Cupcake Batter: In a large bowl, whisk together the flour, sugar, cocoa powder, baking soda and salt. Make a well in the center, and add the sour cream, water, butter and vanilla extract, and whisk until just combined.
Divide the cupcake batter evenly among the 24 liners and top each cupcake with 1 rounded tablespoon of the cream cheese mixture. Bake until the tops of the cupcakes just begin to crack, 23 to 25 minutes. Cool the cupcakes in the pans for 10 minutes, then transfer to a wire rack to cool completely. The cupcakes can be stored in an airtight container in the refrigerator for up to 2 days.