I'm still using EI Universe 5.0, so I believe EI Animation System (5.5) probably has a better Shockwave 3d Exporter since it is a far more recent update.
I don't know how much you know about EI, and what poly count your looking to achieve when exporting to w3d, so let me know?- at the EI forums/site they say that

Amorphium has extensive polygon reduction tools, but I didn't have to do that when exporting to w3d. When I opened up my 1600poly spaceship model in Director (might be a little heavy for older PC's), it was exactly what it looked like in the EI Animator and Director could handle it quite well. The problem was I had no clue how to do Director script, and didn't want to learn, so I scrapped the 3d web/flash project I was going to do.

SleeK

if you know any other programs that have really good polygon reduction systems, I would be really keen to hear it (apparently I like modeling at 5000-10000 when I really need about 500-1500)

Cinema 4D and Lightwave have poly reduction features that are great.