There many 3D modeling and animation software around, like well-known 3Ds MAX, Maya, Lightwave and many others. But most packages are commercial and can cost a lot. However there are freeware too. I know some here are using Metasequoia, GMax, Blender and perhaps some others. So I would like to also inform about another modeling and animation package that has become freeware recently: Caligari trueSpace. It used to be commercial before, but now they made it free. As regards integration with Milkshape it can import/export various formats which can be used to transfer models between them for exporting into Freelancer. Perhaps you might find this one more suitable to your likings, it's always good to find tool that best suits you from the start.
Take a look for yourself and try if you're interested: Clicky!
p.s. among other features it has something really odd (for 3D modeling software that is): real-time collaboration via sort of mulitplayer.
Well, it installed, but now I can't get it to work right... first off, how do you delete stuff, second off, the tutorials use a totally different display than what pops up when I start it, and I think it ate one of my control bars.. the one with prims on it... HALP!