The one mentioned by PP is probably the most accurate. The official My Disney Experience app also lists wait times but only the posted waits and is often glitchy.
That's the million dollar question. The creater of the site frequents the boards, but won't divulge trade secrets I've asked the same thing myself!
FWIW, EasyWDW.com/waits now has the actual wait time as well. So it must be a script that's easy to input, but I'm not tech-savy enough to know where this info is pulled from. From what I understand, it's pretty accurate though. Pretty crazy to look at the wait times and see how inflated the posted times can be....