Hi Ron,
Waterline Systems is still there. They're located behind New England Boatworks(NEB)in Portsmouth (www.neboatworks.com). NEB is a good yard and handles high end racers as well as boats for more 'normal' folk. A few miles across the bay, in Bristol is Allpaint (Allpaint.net) located at the Bristol marine yard. They're another high-end outfit but woth speaking to.
There are a lot of skilled boat types in the area who moonlight or work full time as contractors. It's a bit more complicated since you have to haul at a yard that let's them in but it's doable.
What shape is the bottom in now and what level of quality are you looking for? This area has everything from mom&pop yards to 'world class' facilities. Money can be an issue.