D.W.
I remember being so afraid of thunderstorms as a child - I love them as an adult.
My husband posted some pictures from NASA yesterday on Facebook showing lightening through the volcanic ash from the current Icelandic volcano eruption. They were gorgeous.
As a scientist, I'd recommend taking a basic, but scientific approach to it. He may not understand it, but at least keeping it factual and scientific will help remove some of the fear and mysticism.
DK makes great books (you can get them at Borders/Barnes & Noble) that teach about natural phenomena, you can probably find sites on the internet with lots of great pictures and simple explanations.
http://en.wikipedia.org/wiki/Lightning
http://www.pbs.org/wgbh/nova/sciencenow/3214/02.html
http://www.weatherwizkids.com/
http://environment.nationalgeographic.com/environment/nat...
In the end, I think the best thing is to ask him what part of the lightening/thunderstorm he's most scared of and work through his response. If possible, take him out on a covered porch during a storm, keep some windows open inside to watch a storm pass (unless it's a really serious one) and let him see what happens in a storm as it passes and what's effected by it.
Good luck!