I'm working on Newton 2.0, but the interface chaged a lot, and the documentation is about zero so far.
For hovering, maybe you want to emulate it, but setting buyoancy and water level to the z-position of the point below the hovercraft? Ask in a newton forum for better results.
The vehicle is not too good, and has totally changed in Newton 2.0. I think I'll wait for that. In the meantim you can do what all others do: Create your own vehicle using joints.