Gently handle them. Don't make sudden movements when you're reaching for them in the brooder -- just be patient and scoop them up after you corner them. Hold them firmly, but not too tightly -- they will try to hop out of your hands, so hold them over the brooder. Try to handle them both at the same time so that they won't freak out over being separated.
Next, set them on your lap and keep your hands around them. Stroke them gently.
If you can, try getting them to eat out of your hand. Try keeping them out for five minutes before putting them back, and gradually increase the time that you keep them out of the brooder.
Most of all, handle them frequently so that they get used to you. Talk at them softly and try whistling like adult guineas do.
Due to how wild guineas are, they probably won't ever reach the tame point that chickens are at, but it might help make them less skittish. The friendliest guinea that I have imprinted on me at hatching and was the only chick for a long time, so he got a lot of love, and that's why he's so tame.
Oh, and they are very fast, so have a yardstick handy if there are places that they can skitter under (like the stove). Having another person can be useful, too, if they're being a special pain to catch.
Good luck.