Preheat oven to 350F. Set out a standard sized 12 well muffin tin and fill the wells with cupcake liners.
Using a food processor or a knife, roughly chop the cranberries until you have 1 1/2 cups of chopped cranberries.
In a medium bowl, mix together the flour, baking powder, and salt. Set aside.
In a small bowl rub the sugar and the orange zest together until the sugar is fragrant. Using a stand mixer with the flat beater on medium speed, cream together the butter, cream cheese, and sugar until light and fluffy, 4-5 minutes. Scrape down the sides and add the eggs one at a time, scraping after each addition. Add the vanilla and beat in.
Reduce the speed to low and add the dry ingredients. Beat until just mixed together with a little flour still showing. Take the bowl of the mixer off the stand, add the cranberries, and fold them in with a silicone spatula.
Divide the batter among the 12 wells in the tin. Bake for 25-28 minutes, or until the cupcakes are lightly browned and a toothpick comes out clean. Let them rest for 2-3 minutes, then carefully take them out of the muffin tin and let them cool on a cooling rack. Can be made up to 2 days ahead.