You want to compare apples and oranges (or whatever fruit you like)
Since JOGL is a low level api and if you know what you are doing you can surely get the best performance out of it, but you will have to do everything on your own. J3D is a scene graph and abstracts away the low level functionality. This means it might be easier to organize your games content and to program the interactivity features, but you will get stuck with the capabilities and performance of the scenegraph.
So you have todecide wether you want it easy and structured (J3D) or have the best performance (JOGL/LWJGL) with extra effort of implementing things you get for free when using a scene graph.
Also as a scene graph there are other options than J3D like Xith3D, JME, Ardor3d etc. (others here can suggest some more)
P.S. do not cross post