In the bowl of a stand mixer, combine 3 cups flour, yeast, brown sugar, salt, ginger, cinnamon, nutmeg, and cloves. Add warm water, molasses, and butter. With mixer on low, add additional cup of flour. If mixture is still too wet, add up to an additional 1/2 cup of flour. Beat with paddle attachment until dough starts to form.
Switch out paddle attachment for dough hook and knead dough on medium speed for 5-7 minutes or until dough is smooth and pulls away from edges of bowl.
Shape dough into a ball and place in a large bowl that has been sprayed with olive oil or non-stick cooking spray. Roll dough in the bottom to coat all sides. Cover and let dough rise in a warm, draft-free spot for an hour or until doubled in size.
Preheat oven to 425°F. Line a baking sheet with parchment paper or a silicone baking mat.
Bring water and baking soda to a boil over medium heat.
Turn dough out onto a lightly floured surface. Divide into 6 equal pieces. Divide each piece into 8 equal pieces. You should now have 48 pieces. Shape each piece of dough into a ball.
Gently place 10-12 bites into boiling water at a time. Allow to boil for 30 seconds. Use a slotted spoon to remove bites from water. Place on prepared baking sheet.
Bake for 12-15 minutes or until pretzel bites are golden brown. Remove to a wire rack.
While pretzel bites are cooling, stir together sugar, cinnamon, ginger, and cloves for coating. When pretzel bites are cool enough to handle, dip in melted butter and roll in sugar mixture until coated.
Beat together cream cheese, confectioner's sugar, 2 tablespoons milk, vanilla extract, and salt until creamy. Add additional milk as needed to reach desired consistency. Serve dip with coated pretzel bites.
Best eaten same day. If you have leftovers, store pretzel bites in an airtight container and cream cheese dip in the refrigerator.