I start and use Wings3D, it's free and easy once you understand the basic. http://www.wings3d.com/
But with it you will only make model and uv (and you can export to .obj), for hardpointing ships and export them to .xsi there is XSI mod tool (XSI can import .obj file)
than you need to use XSIConverter to convert .xsi files to .mesh files
There is K-3D, a new free software in development, but the last stable version it's quite impresive.
There is always Blender
More you can read in sins moding documentation, i lost the link but it's somewhere here on forum.