Preheat the oven to 350 degrees F. Line a 12-cup muffin pan with paper liners. Toss the chocolate chips with 2 teaspoons flour in a small bowl; set aside.
Whisk the remaining flour, the graham cracker crumbs, baking powder and salt in a large bowl. Whisk the sugar, melted butter, milk, vanilla and eggs in a medium bowl until smooth; stir into the flour mixture until just combined. Stir in the chocolate chip mixture.
Divide the batter among the muffin cups, filling them three-quarters of the way. Tap the bottom of the pan lightly on the counter to smooth out the batter. Bake until the muffins are lightly browned and a toothpick inserted into the center comes out clean, 20 to 25 minutes. Let the muffins cool 5 minutes in the pan, then remove to a rack to cool completely.
Top each muffin with 1 tablespoon marshmallow cream. Let set 10 minutes.