Combine the apple chunks, cranberries, and cider in a large heavy bottomed pot over medium heat. Bring to a simmer and cook until the apples are soft and the cranberries have started to burst (about 15 – 20 minutes). Set aside to cool slightly.
Ladle the mixture into a food mill and puree. All of the apple and cranberry skins will be left behind. Transfer the puree to a slow cooker. Add the brown sugar to the puree. Slice the vanilla bean lengthwise and scrape out the seeds. Stir in the seeds and the two halves of the vanilla bean along with the cinnamon and ginger.
Cook on low heat in a slow cooker for 8-12 hours, only partially covered. The mixture will reduce down and thicken. Remove the vanilla beans and allow to cool slightly. Transfer to airtight containers and refrigerate. See Notes for canning info.
Notes
Cook time includes time in the slow cooker.
If you want to can this, pour into clean and sterilized half-pint or pint jars and process in boiling water bath for 10 minutes.