Actually, it looks like there is an easier and better solution: use the "lipo" command to remove the i386 code from your existing .jnilib libraries.
lipo libgluegen-rt.jnilib -remove i386 -output libgluegen-rt-64.jnilib
This way you can be sure that your new library matches everything else in your JOGL distribution (whereas if I built it, something might not match up precisely). You'd need to do this for each .jnilib, and then move the old ones out and put the new 64-bit-only ones in their place, using the original filenames. Then you can check with the "file" utility that they're all correct.