Heat oven to 350 degrees.
Prepare cupcake pans by spraying generously with non-stick cooking spray. You could also use cupcake liners, but you do not need them since will be placing these in jars when they are done so just be sure they are sprayed generously.
In large bowl, stir together flour, sugar, cocoa, baking powder, baking soda, and salt. Add eggs, milk, oil, and vanilla extract. Beat on medium speed for 2 minutes.
Stir in boiling water. Batter will be very thin at this point.
Pour into cupcake pans. Fill about 2/3 full.
Bake about 22-25 minutes until toothpick comes out clean. Cool completely before placing them in the jars.
Prepare the frosting: Combine the cream cheese and butter in your stand mixer bowl and mix to combine. Add the confectioner sugar 1 cup at a time, mixing after each addition and using a spatula to scrape down the sides as needed. Add the extract and mix to combine. Place the frosting in a piping bag with Ateco Tip #847.
In each mason jar layer a cupcake with frosting and repeat. You can also cut the cupcakes in half and layer them that way too.