Stuff 1 chocolate chip inside each marshmallow, using a hot metal spoon to make the marshmallow stick to the chocolate and form a very small ball. Place on a plate lined with waxed paper. Transfer to the freezer.
Preheat oven to 350 degrees F (175 degrees C). Grease 2 muffin tins.
Mix graham cracker crumbs with melted butter in a bowl.
Pack graham cracker mixture into the muffin tins with the back of a spoon, creating a crust on the bottom of each cup.
Beat cream cheese and sugar in a bowl with an electric mixer until smooth. Blend in milk. Beat in eggs one at a time, mixing just enough to incorporate. Beat in sour cream, flour, and vanilla extract until batter is smooth.
Fill muffin cups halfway with batter. Place a frozen marshmallow ball in the center of each. Cover with remaining batter.
Bake in the preheated oven until set, 15 to 20 minutes. Let cool completely, about 30 minutes.
Spoon marshmallow cream into a small pot. Heat over low heat until soft, about 5 minutes. Mix in cinnamon and cocoa powder. Pipe frosting over cooled cupcakes.