If you're looking to model, you could try Blender.
There was a post last week by Treewyrn, about MaxLancer. He made some bits and bobs for 3ds Max specifically to help with Freelancer modding. Could be worth looking into.
Yeah Blender is what I see most people using to model ships. But I do not know if they use the same programme to add animation and hard points, pretty sure that's a different programme they use for that.