Here's a pretty nice and FREE 3D Modeler.
http://www.misfitcode.com/misfitmodel3d/
You'll need Pack3D for mass extraction of dats.
And S3D for most other work.
You may need Ref's Terrain Editor if you plan on placeing
Harbors where the water may need deepened or widened.
Gimp seems to be the choice for a free graphics program.
But there are many others out there.
Biggest tool you'll need?
Patience!!!
Lot's of it!!