There are free importers available for Milkshape that will take the stock BC models. But you need Milkshape. You can find those at SFC3files.com I am pretty sure. Additionally, if you have another 3D program, BCfiles.com has the original stock totallygames models available for download in. . . I think it is 3DS format. Also, Darkdrone has the BC stock ships converted on his site.
Otherwise, I know of no program designed specifically for that task.
Hope this helps,
Interstellar Machine