Spring, we have the same problem in the barn but with starlings, and they do their business all over our cars. This is an open barn with exposed structure and trusses, providing lots of nooks and crannies for nests - likely similar to your boat house. We recently sheeted the underside of the roof with some relatively inexpensive 1/4" door skins, and Gary continues to nail sheeting pieces to any remaining exposed cranny. Crossing fingers.
