If you are going to be relocating rocks you need a permit from the Wetlands Bureau. It's a minor impact project so you should use a Standard Dredge and Fill Application to file. You can download the application at
www.des.state.nh.us/wetlands. There is no environmental impact assessment necessary.
You should know the DES is no longer approving the removal of rock from the surface waters, however you may be allowed to move them aside into a similar depth of water where they are not in the way. This change was made at the request of the NH Fish & Game Dept to address habitat loss issues.