Preheat oven to 350 degrees. This will make 24 standard cupcakes, so line muffin tins accordingly.
Beat cream cheese, 2/3 cup sugar to be well blended, but not so much that the cream cheese becomes warm. It's easier to allow cream cheese to come to room temperature and add in sugar and beat lightly.
Add eggs to cream cheese mixture, and fold in chocolate chips.
In a separate large bowl, sift flour, cocoa powder, baking soda salt and remaining 1 1/2 cups sugar.
Mix 1 1/2 cups water with vinegar and vanilla.
Pour half of this water mixture and all the oil into the dry ingredients, and mix well. Add rest of the water, just until mixed.
Fill cupcake liners with 1/4 cup batter, top with 2 tablespoons cream cheese mixture.
Bake for 30-35 minutes (Check at 20 minutes and each five minutes after).
Cool completely in pans before removing.