You don't really say what subjects you wan to shoot. Macro, wrecks, caves, whales, video? Some DSLRs don't have video, and you just might find that a lot of fun. Or not. At the low end, the D5000 shoots video and has a decent sensor, but limits you to AFS lenses, meaning you can't really use the excellent Tokina 10-17mm fisheye that so many prefer for large fish and wrecks. So, think about what you might want to shoot and pick accordingly.
Any housing you buy will be expensive as a previous poster said. I agree, I would not take the D3 underwater. There is a strong chance of flooding it. Since you shoot Nikon, look for an older Nikon with housing, used, perhaps a D70 or D80. They shoot well, just don't have the large display of the current cameras, nor video. The D5000 is good in the middle. Or, step up to a D300S, which will do video and pretty much everything else. Since you are used to a D3, that would probably be the closest lower cost option.
Ikelite makes the least expensive housings by far. They are quite rugged and reliable, but not streamlined like the high end housings. For many, the extra cost is not justified.
I have a hunch Nikon is soon to update most models in its lineup, so don't be in a rush. The recent roll from D3000 to D3100 is the first, and I feel the D300s class might be next, followed by the D90 class. Just a hunch, but if I were Nikon, I'd be looking at Canon's latest products. Canon is releasing so many new models. They have to respond, just a question of when. Of course that will mean some of the current models will go into closeout discounts, which can be attractive. It pays to watch the market for trends and rumors.