I have 3 dogs. 2 males and a female. The boys are not neutered, but get along fine. The female will go after and try to bite the males anytime we yell at them (like leave it, no, etc). She is spayed, and it seems that the aggression is worse now than before she was spayed.

It's reproductive status is meaningless!
TRAINING alters behaviors,NOT scalpels.

Don't yell at your dog. Really it's not doing anything for them. Try-

Muzzling

Head control devices or muzzles can be used with aggressive dogs to prevent bites or other dangerous situations. Do not use the muzzle as a punishment, rather as a precautionary measure. Avoid jerking the dog's head around using either a muzzle or a control collar. Gentle tension and positive praise for good behavior will work for most dogs. pets question and answers,www.5d2d.com

Good Luck!

"Spaying in female dogs removes the production of progesterone, which is a natural calming hormone and a Serotonin uplifter. Spaying may therefore escalate any observable aggressive behaviour, either to humans or other dogs."
http://en.wikipedia.org/wiki/Neutering

The female is going to be aggressive with the two males because that usally how dog "fall in love" with each other the dogs fight witch means that the dog is trying to get the other dog.

Happend to me like 3 mounths ago with my dog and a new dog i brought home

Training and obiedience.