I have a D90 (basically the previous generation of the D7000) and an OM-D E-M5. I find that, when running out the door, I tend to grab the OM-D. The Nikon has slightly better dynamic range, slightly faster focusing, and I'm more used to the Nikon shortcuts to adjust settings. My impression is that lenses of the same quality are cheaper for the Nikon, but smaller and more portable for the Olympus (for example looking at good-but-not-great fast normal primes, the Nikkor 35mm f/1.8 is US$200, while the Panasonic 20mm f/1.7 is US$300), but it's really hard to compare lenses of similar quality. The OM-D is smaller and easier to carry around for those times when I'm not photographing, and that single fact outweighs the minor performance advantages of the Nikon. The one area where the OM-D significantly outperforms Nikon is with the image stabilization, but that's not much of an issue underwater.
An added advantage is that, with either the 60mm macro or the 8mm Zuiko fisheye and MMF-3 adapter, the OM-D is splashproof so a minor housing leak won't be an issue. I don't know if there's another splashproof fisheye lens for the MFT mount, I own the four-thirds 8mm so I just use it with an adapter.
In the end, I'd get the OM-D. It's more fun, and image quality is similar. My only advice is to get it without the 12-50 kit zoom. I find that lens to be awful, even compared to other kit zooms. I never thought contrast would be an issue with a modern lens, but the 12-50 has such poor contrast that images often appear to be blurry.