In a small bowl, mix the honey, warm water, and yeast until the yeast begins to bubble.
In a medium bowl, mix the whole wheat flour, 1 3/4 cups all-purpose flour, salt, and olive oil with an electric mixer on medium speed. Pour the yeast mixture into the flour mixture and continue to mix on medium speed until a smooth dough is formed. If dough is too sticky after 5 minutes of mixing, add flour by the teaspoon until the dough pulls away from the sides of the bowl.
Spray a large bowl with canola oil cooking spray. Place dough in the bowl and cover with plastic wrap. Let dough rise until it has doubled in bulk, about 1 hour.
With clean hands, punch down the dough. Sprinkle a clean work surface with the remaining 2 tablespoons of flour and pour the dough onto the work surface. Lightly knead dough for 1 minute.
On a pizza pan or baking sheet covered with parchment paper, shape dough into desired shape.
Preheat oven to 425 degrees F.
In a medium bowl, mix drained crushed tomatoes and tomato paste. Add oregano, basil, and pine nuts and stir until combined. Spread tomato mixture on top of dough. Top with shredded cheeses and bake for 20 to 30 minutes, or until cheese is melted and bubbly.