Preheat oven to 350°. In a small bowl, beat cream cheese, sugar and flour until smooth. Beat in egg. Stir in 2/3 cup chocolate chips. In another bowl, toss coconut with pecans and remaining 1/3 cup chips.
In a large bowl, whisk together the first 5 batter ingredients. In another bowl, whisk together coffee, oil and vinegar; add to dry ingredients, stirring just until moistened.
Fill paper-lined muffin cups half full with the batter. Place scant 1 tablespoon cream cheese mixture in the center of each. Top with about 1 tablespoon coconut mixture.
Bake until a toothpick inserted in the center comes out clean, 20-25 minutes. Cool 5 minutes before removing from pans to wire racks to cool. Serve warm.