Preheat oven to 350 F.
Cut squash in half lengthwise and scoop out seeds. Brush interior of squash with olive oil and apple cider vinegar. Sprinkle with salt and pepper. Place squash halves skin-side up on a parchment or foil-lined baking sheet. Bake for 1.5 - 2 hours. Let cool for at least 15 minutes.
While the squash is cooling, prepare the stuffing. Combine the quinoa and stock in a saucepan and bring to a boil. Cover, reduce heat to low, and simmer for 15 minutes. Fluff with a fork and set aside.
Season the onion with salt and pepper and sautee over medium heat until fragrant and soft. Add apples and sage leaves and cook for 10 minutes until apples are soft.
Add cranberries and continue stirring mixture for 10 minutes. Add quinoa and pumpkin seeds, mix well, and remove from heat.
Generously fill each squash boat with stuffing and return to oven for 5-10 minutes before serving.