Prep the pan. Line a 12-cup muffin tin with paper liners.
Preheat the oven to 325°F (165°C).
Make the crust. In a bowl, mix graham crumbs, melted butter, sugar, and salt until the texture looks like wet sand. Divide the mixture among the cups (about 1 heaping tablespoon each). Press firmly with the bottom of a small glass or spoon.
Pre-bake the crust. Bake for 5–7 minutes until just set.
Remove from the oven and cool slightly.
Beat the filling. In a large bowl, beat cream cheese and sugar until smooth and fluffy, about 1–2 minutes. Add Greek yogurt, vanilla, lemon zest, and salt, and beat until combined. Add eggs one at a time, mixing on low just until incorporated.
Do not overmix.
Fill the cups. Divide the batter evenly among the crusts, filling each about 3/4 full.
Bake. Bake at 325°F (165°C) for 16–20 minutes, until the edges are set and the centers still wobble slightly. They will finish setting as they cool.
Cool gradually. Let the cheesecakes cool in the pan on a rack for 30 minutes. Then transfer to the fridge to chill for at least 3 hours, preferably overnight.
Cook the cranberry topping. In a small saucepan, combine cranberries, sugar, water or orange juice, orange zest, vanilla (if using), and a pinch of salt.
Bring to a simmer over medium heat. Cook for 8–10 minutes, stirring occasionally, until the cranberries burst and the sauce thickens. Taste and adjust sweetness.
Cool completely; it will thicken more as it cools.
Top and serve. Spoon cranberry sauce over each chilled cheesecake cup. Add whipped cream and garnish with pistachios or a bit of candied orange peel, if you like.