Nautical imagery occasionally appears as a symbol for – well, we're not quite sure what, but going from everything else in the story, it probably has to do with confusion and lack of knowledge. The Governess first alludes to ships when she arrives at Bly and comments on how strange it is that she should be metaphorically steering the household, which she compares to a "great drifting ship" (1.9) full of lost passengers.
Boats make an appearance in both of the scenes at the lake with Flora, and possibly symbolize her deception of the Governess. First, the little girl attempts to build a little toy boat out of wood while the Governess, horrified, sees the ghost of Miss Jessel for the first time. In the return to the lake, Flora somehow manages to abscond with the rowboat that's usually docked at the lake and move it to a more hidden location; there's never any explanation of how or why she does this by herself, but the Governess takes it to be another sign of her dishonesty.