There are a number of programs that you can use to model ships for Freelancer, though the best program for finishing them and implementing them into the game is probably Milkshape. Some of the programs people use are:

GMax - GMax is nice because it is free and fairly powerful, however it takes some getting used to and plugins are sometimes hard to find.

Milkshape - Milkshape is a very simple program to use though in the hands of a skilled user it can create models with quality of much more expensive programs. Plugins are numerous and easy to find, and Milkshape can export straight to Freelancer. It will only cost you $20 to register the program for life, and a free 30 day trial is included.

Lightwave - Lightwave is one of the most powerful 3d modeling programs available. It is quite expensive though and creates models that are very high in polycount. Plugins also cost money and the interface will take some getting used to.