In a large bowl, whisk together flour, brown sugar, cocoa, baking soda, cinnamon, and remaining chocolate chips.
Stir in the coffee, oil, and vinegar, and mix until wet and dry ingredients are just combined.
Line regular-sized muffin cups with paper liners.
Fill half full with muffin batter.
Drop a rounded tablespoonful of cream cheese mixture onto the top of the batter.
Sprinkle with a tablespoonful of coconut-pecan mixture.
Bake at 350 degrees for 20-25 minutes, or until a toothpick inserted near the center comes out clean.
Remove to a wire rack to cool for 10-15 minutes before serving. These are wonderful served warm, but just as wonderful when they've cooled completely.