In a small mixing bowl, combine the peppercorns, thyme, bay leaves, cloves, garlic, and whole juniper berries. In a saucepan, over medium heat, combine the water, brown sugar and salt. Bring to a boil and stir to dissolve the sugar and salt. Remove from the heat and add dry spice mixture and steep for 1 hour. Place the brisket in a glass or plastic container. Pour the seasoned brine to cover the brisket completely. Cover and refrigerate for 3 weeks, turning the brisket every couple of days.
Preheat the smoker according to the manufacturer's directions.
Remove the brisket from the marinade, and pat dry. Discard the marinade. Combine the remaining 1/3 cup crushed juniper berries and ground black pepper in a small bowl. Using the palm and heel of your hand, press 2/3 of the berry and pepper mixture into the brisket. Press the remaining mixture into the other side. Place the brisket in the smoker and smoke for about 4 hours. Remove from the smoker and cool for 30 minutes. Remove from the pan and cool completely. Slice into thin slices and serve.