Had the same thing with my Tommy, a Patterdale Terrier who I had since he was an 8 week old pup. He started off boating with no problem at all, and spending time in the cabin to begin with as he joined me in January 2016 and it was flipping cold!
Something must have changed in his attitude though as one day out of the blue he decided he didn't like the noise from the engine room whilst sitting in the back cabin. By this point he was a few months old and the start of summer so he came out to join me on his bed I'd placed on the slide. He is more than happy now and spends his time relaxing on the bed watching the world go by. It's also nice to have company whilst boating and there's always an appropriately placed ear to scratch
Another problem he had was when I'd pull in to carry out a delivery and would leave the tiller to shift coal or pump diesel or whatever. He'd scream and shout until I'd return, the same applied but unfortunately worse when I'd take coal or drums of diesel off in the wheelbarrow.
I made the mistake of turning around to him and saying "shush" etc but soon realised he was getting what he wants. I then tried ignoring him, if you can mamage to put up with yapping and barking for a short time, the dog gets bored with no reaction and shuts up. Tommy certainly did and when I go off delivering I can sometimes be delayed half an hour or so whilst chatting to customers and when I return Tommy is sat as good as gold waiting for me.
Ignore any bad or unwanted behaviour and reward any good or positive behaviour. It definitely works. Don't forget that our canine friends are excellent at picking up our own moods so if you are nervous and hesitant then the dog will be too.