Heat oven to 350 degrees F. Line 2 standard-size muffin pans with 24 cupcake liners.
In bowl, mix flour, cocoa, baking powder, baking soda and salt. In second bowl, beat butter and sugar on medium-high until smooth. Beat in sour cream. Beat in eggs, one at a time. On low speed, beat in flour mixture and food coloring, alternating with milk. Spoon into cupcake liners, filling each about 2/3 full.
Bake at 350 degrees F for 23 minutes or until toothpick inserted in centers of cupcakes comes out clean. Remove from pan; cool completely on wire rack.
Beat Neufchatel and butter until smooth. On low, beat in confectioners' sugar, then vanilla. Spread or pipe onto cupcakes.