There are outfits that will weld and repair wheels. I used one to fix a nice big dent in my FJR's front wheel (thanks for the $200 pothole, California!)
There are no Ninja 1000 rear wheels available on ebay at this time. The parts numbers for several models are similar but not exactly the same. A couple of wheels are available from ZR6's and a Ninja 650R. These look identical but no way for me to know for sure without buying and shipping one. A little expensive gamble. Will keep looking. If anyone know if one of these wheels will fit please let me know....This happened to me once on my R6, front wheel. I bought a new condition used wheel off eBay including rotors for MUCH cheaper than a replacement wheel alone (which needs everything bearings, seals, rotors, valve stem).
Look up the wheel part # and see if any other bikes use the same one, it will widen your search pool.