Preheat the oven to 350°F.
Line two muffin tins with paper cupcake liners.
In a medium bowl, stir together the cream cheese and sugar until smooth.
Add the egg, vanilla, and salt and stir until smooth.
Stir in the chocolate chips.
Place the cheesecake filling in the fridge to firm up a bit while you prepare the cupcake batter.
In a large bowl, whisk together the flour, cocoa powder, sugar, salt, and baking soda until well combined.
In another bowl, whisk together the water, oil, vanilla, and vinegar until combined. Pour this mixture into the dry ingredients and stir until just combined.
Fill the prepared muffin tins with the cupcake batter until they are half to 2/3 full.
Place 1-2 tablespoons of the cheesecake filling on top of each cupcake (I like to use a 1.5 tablespoon cookie scoop for this).
Bake for 20-22 minutes, or until a toothpick inserted into the chocolate part of a cupcake comes out clean.