Preheat the oven to 350 degrees and line 16 muffin tins with cupcake wrappers.
For the cheesecake filling
In a medium bowl, beat the softened cream cheese, egg, and sugar until smooth with no lumps.
Fold in the chocolate chips until fully incorporated and set aside.
For the cupcakes
In a large bowl, sift together the flour, sugar, cocoa powder, baking soda, and salt.
Make a well in the center of the mixture and add in the water/coffee, oil, vinegar, and vanilla.
Whisk together until well blended.
Using a cookie scoop (to make your life easier), fill each muffin tin half way full with batter. Top with a tablespoon of the cream cheese mixture. {I had a little cream cheese mixture left over so I just went around the tins again and added more to each cupcake until I was out}
Bake for 25-28 minutes or until the tops spring back when you lightly press them.
Cool for about 5 minutes in the pan before you remove them.