Make the dough: Pulse the whole-wheat flour, all-purpose flour, granulated sugar, vinegar, salt and about one-third of the butter in a food processor until the butter is incorporated. Add the remaining butter and pulse until it is in pea-size pieces. Add 2 tablespoons ice water and pulse until the dough just comes together. Pinch a small piece of dough: If it doesn't hold together, add up to 2 more tablespoons ice water, pulsing, 1 tablespoon at a time. Turn the dough out onto a large piece of plastic wrap and press into a ball. Pat into a 1/2-inch-thick disk and wrap tightly. Refrigerate until firm, at least 1 hour.
Roll the dough into a 12-inch round on a lightly floured surface or between 2 pieces of lightly floured parchment paper. (If the dough becomes soft, refrigerate until firm.) Center the dough in a 9-inch pie plate. Fold the overhang under itself and crimp the edges; refrigerate 30 minutes. Meanwhile, preheat the oven to 350 degrees F.
Lightly pierce the bottom and sides of the crust with a fork, then line with parchment paper or foil and fill with pie weights or dried beans. Bake 20 minutes, then remove the parchment and weights and continue baking until lightly golden, about 10 more minutes. Transfer to a rack and let cool completely.
Meanwhile, make the filling: Bring 3 cups blueberries, 1/2 cup granulated sugar and the lemon zest to a simmer in a saucepan over medium heat, crushing the berries slightly with a wooden spoon. Cook, stirring occasionally, until reduced by half, about 20 minutes. Discard the lemon zest. Transfer the blueberry mixture to a bowl; stir in the remaining 3 cups berries and 1/4 cup granulated sugar, the lemon juice, whole-wheat flour, nutmeg and salt. Let cool completely.
Make the topping: Combine the nuts, brown sugar, whole-wheat flour, butter and salt. Squeeze the mixture into clumps with your hands and scatter on a baking sheet. Freeze 30 minutes.
Increase the oven temperature to 375 degrees F. Pour the blueberry filling into the crust and top with the frozen crumb topping. Transfer to a baking sheet and bake until the filling is bubbly and the topping is golden brown, 45 to 55 minutes. (If the topping browns too quickly, cover it with foil.) Transfer the pie to a rack and let cool overnight, or at least 4 hours, so the filling sets.