In Earth's atmosphere, Thor can fly at Supersonic speeds (410-1,710 m/s), but able to travel faster than light if in space. Diana on the other hand has been said to be able to fly at speeds approaching half the speed of light (149896229 m/s). If I were to take a guess, she can travel much faster than Thor if they're fighting in earth's atmosphere, but in space he's going to have a big advantage.
Wonder Woman could also use her bracelets to deflect Thor's lightning if I'm not mistaken, and with her incredible speed, and also her reflexes being noted by Batman to be superior to Superman's, she could probably dodge his attacks anyway.
Thor also can't just shoot lightning willy nilly, he has to manipulate natural storms using Mjolnir; so if there's already a storm going on in the area? Great, fire away Thor; if not, he would have to first summon stamp the handle of Mjolnir twice onto the ground to summon the elements of storm (this is how it works to my understanding at least), and if he had to drop down to the ground to do that, Wonder Woman would take that time to rek him.
To my current understanding of these two, I think that Wonder Woman comes out on top in just about every field, even with as strong and fast as Thor is, I'm pretty sure she's still stronger and faster.
edit: thinking back, Thor could be stronger. Not sure, hoping Zal or someone else has more insight than I do!
Last edited by Gollum on Mon Feb 29, 2016 7:17 am, edited 2 times in total.