Whisk together the pudding mix, milk, and vanilla extract in a large bowl according to the package directions. Let stand until set, about 5 minutes. Fold in the Cool Whip.
Arrange one sleeve of graham crackers in the bottom of a 13- x 9-inch baking pan or dish. (You may need to cut or break some of the graham crackers to fit into the pan.)
Top the graham crackers with half of the pudding. Top with another sleeve of graham crackers in a single layer.
Repeat the process with the remaining pudding and ending with the final sleeve of graham crackers on top. Refrigerate for 1 hour.
Meanwhile, make the chocolate ganache topping: Pour the chocolate chips into a medium bowl. Heat the cream in a medium saucepan over medium heat until bubbles form around the edges. Pour the cream over the chocolate chips and let stand for 5 minutes. Stir until the chocolate is smooth.
Let the ganache stand or refrigerate until slightly thickened and spreadable. Pour over the graham crackers and spread in an even layer to cover. Refrigerate overnight.
Remove the cake from the refrigerator and cut into squares before serving.