In my experience it's easier to pry the rubber off the body. The installation procedure calls for the gasket to be put on the glass first, then pulled over the body flange with string. The gasket is designed to be a very tight fit on the glass, and very stiff on the outer edge, but quite soft and pliable on the inner edge.
The very easiest and safest way to do it if you're replacing a broken window with a salvaged one is to cut the gasket off the good window and replace it with the one from the broken one, but if you're just removing to do body work, try gently pushing out the gasket at one corner from the inside, and working it off gradually along whichever edge (bottom in the case of an XJ) is the longer. It helps to have two people so that if it releases quickly it doesn't fall on the ground, but if you're alone, you can get it out a certain way and it will hang, then you can get outside and pull rather than push. As you get more of the gasket off the body flange, it becomes progressively easier to pull it without stressing the glass. Once one edge and a little of the ends is free, try pulling the glass sideways toward that edge more than outward. Basically what you want to do is slide it sideways out of the tapered hole.
