-( Story related, cannot be missed )-
*What I'll be describing is the way I managed to get it, which was on Very Easy. If there are differences that have to be added, please let me know. Please elaborate why you down-vote the solution.
(Very Easy difficulty, using the EZ Gun)
The final boss fight in this game is against The Boss, otherwise known as The Joy. The battlefield will be more in her advantage, especially with her choice of camo, but you can also use this to your advantage should you have obtained the Snow camo earlier (before fighting The Pain in the same screen of the cave).
She'll start the battle by rushing towards you. Once she gets close, the traditional shock mark (!) will appear over Snake's head. You have a split second to press
to counter her CQC attack, which will do a bit of stamina damage to her and throw her onto the ground. Use this time to gain some distance between the two of you, hiding behind a tree. She'll pop right back up and seek shelter herself for a bit. As she's hiding, this is your chance to change hiding spots. If you remain out of her sight, she'll comment on where you went and make her way to where you were last seen. Line up your shot from your hiding spot to get three good shots on her, felling her.
If you repeat this process, you'll easily down her with little damage dealt back to you. If she's aware of you and is shooting at you, you will be unable to do any damage to her. Furthermore, if she manages to rush you, you either counter her attack or she will do a decent chunk of health damage to you every time. However, you could also do some CQC damage to her when she's up close and you feel more confident using that.
*Notice: If you're going for the stamina kills for all of the camouflages, make sure you finish her stamina off with her being somewhat near you. You only have about five to seven seconds after prompting the camo drop to pick it up. She drops the SNAKE camo.