1Preheat oven to 350 degrees F (175 degrees C). Line two 12 cup muffin pans with paper liners. Sift together the flour, baking soda, cocoa powder and salt. Set aside.
2In a large bowl, whisk together 1 cup sugar, oil and water until blended. Stir in the vinegar and vanilla. Beat in the flour mixture until incorporated. Set aside.
3In a medium bowl, beat together the cream cheese, egg, 1/3 cup sugar and salt. Stir in the chocolate chips.
4Fill muffin cups 1/3 full with chocolate batter, then top with a heaping tablespoon of the cream cheese mixture. Bake in the preheated oven until the tops spring back when lightly pressed, 20 to 25 minutes.