Well, firstly, The Boss outclasses Snake in CQC, so it’s best if you avoid tangling with her. The most effective way of beating her is probably to duck down in the long white grass, and equipped yourself with the Mosin Nagant. The long grass will provide you with the necessary cover, and you can then use the Mosin Nagant to pick her off whenever she appears. Note: You can usually find her hiding behind the trees.
Oh, and as Mappy said – Stun grenades are also very effective too.