If it works well, why are you looking to replace it? My general feeling is that lenses, rigging, lighting equipment, and audio equipment are all better investments for any kind of filmmaker to improve your films than updating a good camera that still works well. Especially if we're talking about a DSLR to be used for stop motion, where you're able to shoot in super high quality at very high resolutions compared to anything you would use for a final 1080p product. It's just a lot of money to spend for no noticeable improvement.
Also, unless you already own some expensive electronic Nikon lenses, if you really do need to upgrade I would encourage you to look at cameras besides Nikon, because Nikon cameras have an extremely long flange on the lens mount, which means they can use very few lenses beside Nikon lenses. Canon cameras, on the other hand, can take mostly any lens. And it's really not that hard to learn a new DSLR, they tend to be pretty similar in design and function. Especially Canon and Nikon.