Cream Cheese Filling: In your electric mixer, or with a hand mixer, beat the cream cheese until smooth. Add the sugar, egg, and vanilla extract and beat until creamy and smooth. Set aside while you make the Chocolate Cupcake batter.
Chocolate Cupcakes: In a large bowl sift together the flour, sugar, cocoa powder, baking soda, and salt. In a separate bowl mix the water, oil, vinegar, and vanilla extract. Make a well in the center of the dry ingredients and stir in the wet ingredients until nice and smooth. Evenly divide the batter among the 12 muffin cups. Then place the cream cheese mixture into piping bag, pump the cream cheese filling into the center of each cupcake.
Bake in the preheated oven for about 25 minutes, or until the cream cheese filling has set and the cupcakes feel springy to the touch (a toothpick inserted into the chocolate part of the cupcake will come out clean). Remove from oven and place on a wire rack to cool. The cupcakes can be covered and stored in the refrigerator for about 3 - 4 days.