Line 18 muffin cups with paper bake cups; set aside.
In a small mixing bowl beat cream cheese with an electric mixer on medium speed until smooth. Add 1/3 cup of the sugar and the egg product. Beat on medium speed for 1 minute or until smooth. Stir in the semisweet chocolate pieces; set aside.
In a large mixing bowl combine remaining 1 cup sugar, the flour, cocoa powder, baking powder, baking soda, and salt. Add water, oil, vinegar, and vanilla. Beat with an electric mixer on medium speed for 2 minutes, scraping sides of bowl occasionally. Spoon batter into the prepared muffin cups, filling each half full. Spoon about 1 tablespoon of the cream cheese mixture over each. Sprinkle with granola.
Bake in a 350 degrees F oven for 25 to 30 minutes or until tops spring back when lightly touched. Cool cupcakes in pan on a wire rack for 10 minutes. Remove cupcakes from pan; cool thoroughly on wire rack. Makes 18 cupcakes.