Our dog is/was the same, but as previously said stick with it, it gets better. We've had our boat for just over two years now and on a recent trip he even lay down on the stern locker and slept, that was a first! We have a semi trad and he has his preferred place!
He hates tunnels so I go down inside with him and he sits (still trembling!) on my lap, some locks he comes with me, some he stays on the boat, depends how busy it is, he doesn't like them but he's much better than he was. Good luck!