1. Preheat oven to 350ºF. Prepare muffin pan by lining with muffin liners or by spraying with cooking spray.
2. In the mixing bowl of a stand mixer, beat together the ingredients for the filling (except the chocolate chips) until light and fluffy. Gently fold in the chocolate chips. Set aside.
3. For the cupcakes, in a large bowl, mix together flour, sugar, cocoa powder, baking soda, and salt.
4. Make a well in the middle of the dry ingredients and add in the water, oil, vinegar, and vanilla extract. With a whisk or wooden spoon, mix together the dry with the wet ingredients until well combined.
5. Fill muffin cups with 2/3 full of batter then spool 1 level tablespoonful of filling into the center of each cupcake. Repeat until all batter and filling have been used up.
6. Bake 20-25 minutes or until cake portion comes out clean with a toothpick. Let cupcakes cool in pan for 5 minutes before removing and transferring to wire rack to cool completely.
7. Store in an airtight container.