It seems to be a preference thing and possible environmental thing, honestly. You'll find people who believe each method is superior.
I know that personally, I have coded since the green-on-black and amber-on-black terminals were around, and now I use light gray text on black backgrounds wherever possible. I find black backgrounds to be extremely comfortable on my eyes even for very long sessions, but white backgrounds are very fatiguing. I have heard it described as "staring into a 100 watt lightbulb" and that's how it feels to me.
Room lighting can potentially have a significant effect also. Brighter rooms may lend themselves to brighter backgrounds, and darker rooms to dark backgrounds. It reduces the need for your eyes to struggle to switch between wide and narrow pupils required for bright then dark then bright as you occasionally look away from the monitor to relax your eyes (you should always do this, right?).
The best advice is to just try both, give it a week or so, and decide which you like better. If you find both the extremes are glaring, try using a more subdued theme than pure whites and pure blacks, try some softer grays.