Indeed - i model/unwrap in c4d and export as fbx file load it up with 3dsmax 7 and use a script (stock obj exporters ALL suck)http://www.guruware.at/main/objio/index.html
for importing/exporting the obj models (preset is Lightwave*).
As for texturing, photoshop and gimp (gimp to create the games "custom" png's with specular in alpha channel.
Buying c4d just for low poly ships would however be way overkill
Just as extra, the textures are actually quite complex to make
I use a mix of my own (surface) renderings made with c4d and freestyle drawing in photoshop, lots of editing, merging, mirroring cloning and such... This means my textures are maybe not the way "professional" artists would do them, but i like them and they are done quickly (once you have enough "source" surfaces rendered