Bring a medium pot filled with a couple inches of water to a simmer. Set a heatproof bowl on top, making sure the bottom is not touching the water. Add the cream cheese and sugar to the bowl and stir to incorporate, then let melt.
Meanwhile, add the water and gelatin to a small bowl and let bloom until the water is absorbed, 2–3 minutes.
Once the cream cheese softens and turns off white in color, add the lemon juice, vanilla, and lemon zest. Whisk to incorporate and remove any lumps.
Add the bloomed gelatin to the cream cheese mixture and whisk until fully melted and incorporated.
Remove the bowl from the double boiler and freeze for 5–10 minutes, until cooled.
Remove the cream cheese mixture from the freezer and gradually fold in the whipped topping until well incorporated.
Scoop the filling into the mini graham cracker crusts. Freeze for 15 minutes, or until completely set.