On the level with the exploding dynamite Boss, sneak around and hide so that he does not see you. Note: Bongo music will play when he is on your tail. Then, shoot him with the rifle in the back. This surprises him (the game will say "You surprised him!"). Then, power on through with as many shots as possible to get his life down. Repeat the hiding routine, then sneak shot again. Do npt use combos, as they do not really effect him much. Just power on through with single shots; because the first one stuns and the successive ones hurt him. Also, when he is on your tail and is going to blow you up, do a sidestep or one of those rolls to get out of the way. The area with the low cement walls works well if you duck down.
You can also climb on top of the roof of the house in the center of the village, then climb on top of the shack. From this point, you can stand there and not worry about being hurt by the dynamite, and the Boss will not be able to see you. He will keep walking the same path repeatedly. This makes it easy to "surprise him" several times to kill him.
Climb up on the peak of the shack. Stay on the highest point of the roof. He will soon start attacking, but you are too high and out of range of his dynamite. Every time he attacks, the explosion blows him back. Shoot him in the head and chest with your rifle. It is easy to wear him down this way without using your health. When your rifle runs out of ammunition, use your pistol. He will be done for good.