If your intention was to exclude the boat, then by all means crop the photograph--if the proportions of the remaining space and the relationship of every space to every other space is as necessary as it would have been had you not cropped. Think of the "subject" as everything in the picture and the relationship of each object or space to each other, and not just the things--beach, clouds, tree.
Trim the print to eliminate the boat. Otherwise, as someone has already pointed out, someday someone will remove your overmat, discover the boat, and, assuming the photograph is not as good with the boat, attribute a failed effort to you. Trim the print and leave space between it and the overmat. In my experience, when folks use overmats right up to the edges of the print they invariably cover part of the photograph, even if it is as little as 1/16 of an inch. And almost just as invariably, the complete image they saw on the ground glass is better than the slightly cropped one.
Below is something I wrote earlier about cropping. Those who have not seen it before may find it useful.
There is no right or wrong regarding cropping, But at the risk of being labeled a fanatic, I will quote myself: "Cropping is an admission of failure to see creatively." That being said, when the finished photograph is viewed no one (and I include myself here) ever asks or cares whether or not it was cropped. And certainly if the subject you are photographing does not fit the film format, then by all means one must crop. Although when cropping is done in this way I do not consider it cropping because essentially the photograph was seen before the negative was exposed--it just did not fit the film format. What I think of as cropping occurs when in the darkroom one realizes that, for example, the left side is irrelevant and needs to be eliminated to make the photograph better.
For me the highest thrill in photography is the intense way I engage with the world when I am making the photograph. When the image feels "right" on the ground glass, exactly right, there is a great feeling of intense pleasure. There is also some measure of personal growth, but a discussion of that is for another time. Then later, after having made and studied rough proofs of everything, when I am in the darkroom the decision is simply: to print or not to print.
Falling back on cropping as one's normal way of working deprives the worker of the intensity of the engagement with the world. For one who works like this, if the image does not look quite right on the ground glass, they needn't worry about it; it will be fixed later. Not only is intensity, and consequently growth of vision, minimized or eliminated, but longer hours must be spent in the darkroom making decisions on exactly how to crop. For myself, I prefer to make those decisions in the field.
Over 20 years ago I dry mounted labels to the back of photographs for a portfolio of 8x20-inch contact prints I was making. To position them I used what was essentially a small (3" x 6"opening) overmat. One day I found this small overmat on top of one of my photographs; inside the opening was a beautiful small picture. I then moved the overmat around the photograph and found about a half-dozen other beautiful small pictures that, when cropped out and mounted would be quite lovely. Why not crop them out and mount these small gems? The only reason I could come up with was that I did not have enough time. But recently I have been thinking that someday I may make an entire series of photographs out of that one 8x20.