Preheat oven to 350 degrees. Line 18 cups with cupcake liners
In a heatproof bowl, mix together cocoa and boiling water, next mix in buttermilk.
In a large bowl use an electric mixer, beat butter and sugar on medium high until fluffy (apprx 3 min)Add eggs one at a time beating after each egg, until combined Add food coloring, vanilla, and alt, beat until combined.
Add half the flour and beat on low speed. Once combined add the other half of flour and beat until combined on low.
In a small bowl stir together the baking soda and vinegar and quickly stir the mixture into the batter with a rubber spatula.
Fill cupcake liners 3/4 full. Bake in oven for apprx 18 minutes until centers are set. Remove from oven and set on wire racks until cool.
Cream Cheese Frosting:In a bowl with an electric mixer, beat cream cheese, butter and vanilla on medium high until light and fluffy. Sift in powdered sugar 1/2 cup at a time and beat well between each addition. Frost cupcakes as desired. If too soft, refrigerate frosting for 10-15 minutes.