First I need to say I'm really sorry it took so long to get back to you. My computer crashed and between trying to get it fixed and dealing with a new computer it's been extremely frustrating.
I did try to do some research on Pilonidal Cysts and I was shocked to find that there really isn't any real home remedy suggestions anywhere. I do know how awful it is to go through this. It's extremely painful and to get relief it is horrible pain to have it drained. Many years ago a friend of mine went through this and told me how awful it was.
If I was dealing with this I'd try mixing sea salt with hot water and soaking a washrag than apply the compress to the infected area several times a day. The salt should help sooth the cyst and pull the infection out. Salt is a lot more medicinal than people realize. I'd also apply some Black Salve to the area daily. Black Salve is known to draw infection from the skin. I'm really not sure if this will work but I think it's well worth a try before having it drained. Black Salve is very inexpensive and goes a long way.
If you can't find the Black Salve in your area you can buy it at: http://www.mynsp.com/grandmasherbs