Preheat the oven to 400 degrees F. On a large, rimmed baking sheet, toss the sweet potatoes, apples, shallot, and garlic with the olive oil. Roast until tender, 20 to 30 minutes.
In large saucepan, bring the water to a boil. Add the quinoa. Reduce the heat to low and simmer until the water is absorbed, 17 to 20 minutes. Remove from the heat and fluff with a fork.
In a large bowl, combine the quinoa and roasted vegetables. Add the toasted hazelnuts, dried cranberries, lemon juice, thyme, cinnamon, ginger, and some salt and pepper.