You really can’t. Java3D is a SceneGraph while JOGL is a graphics library. A SceneGraph is usually implemented using a graphics library. You can compare JOGL with DirectX while Java3D is more comparable with a Game-Engine (at least conceptual) and is designed to hide the lower level aspects like actually drawing something. In JOGL you would write code to draw a triangle while in Java3D you would specify a Triangle object and place it in the scene which is organized as an object tree (roughly comparable to a hierarchical file system).
So ask yourself if you want to get your hands dirty for full control and flexability (JOGL) or use a ready made framework, which can result in more productivity (once you’ve overcome it’s learning curve) but is more or less fixed in it’s featureset. (Java3D)
If you know 3D graphics from modeller-applications you might better get along with a SceneGraph. If you want to know the fundamental mechanics of 3D graphics, use JOGL.