I'm trying to get the 16-bit integer unsigned value for a pixel in an image using JAVA.
int d = img.getRGB(x, y);
I don't have experience with image manipulation in java, but from the javadoc you should be able to get a Raster object from the method getRaster(), then either getPixel(x,y,int arr) or getDataElements(x,y,object outData) may work.
That assumes that the image is in 16 bits format in the first place. If not you will need to convert the RGB value to 16 bits. This question may be relevant in that case: How to convert between color models