You should never use the phrase "best" with any program
You could get several answers as to what the "best" program to make SEIV shipsets is, and they could range from your standard Microsoft Paint, to the Moray/sPatch/Povray combo (all can technically be used free), to some $2k professional graphics program.
I'm going to assume you want free, so you should probably try Moray/Povray:
www.povray.org www.stmuc.com/moray
and you should be able to find out where to get sPatch from those sites, makes more organic looking models...
Or, Blender:
www.blender.nl