Recreational boaters like their bilges dry. Wet bilges are smelly and unhealthy. Most recreational boats of any size have multiple automatic bilge pumps to ensure that water doesn't stay in the bilge for long.
The cooling water that flows through my engine or my HVAC system is water that was sucked into their cooling systems only moments before. If it is depositing "non-native species" into the water (and they would have to be pretty small to get past the strainers), those same species were already there.
The "gray water" that flows from sink drains and shower sumps is fresh water -- the same water I drink and brush my teeth with. Unless the municipalities that supply that water have screwed up big time, it contains no "species," non-native or otherwise.
This is not a small issue for a recreational boat owner. When I take my boat North from Maryland to Maine next summer, I will, depending on my route, pass through the waters of as many as nine different states. A trip South to Florida in the winter would take me through the waters of five different states. That adds up to a lot of money to address a "problem" that, as far as recreational boaters are concerned, is a non-issue.
Two different questions
Trailer Boats are Responsible for introducing nuisance species to other areas. (Such as Milfoil in Southern Maine)
How to deal with the issues of small craft versus large commercial craft is another. We all play a part in preventing the proliferation of non-native species. However I don’t believe requiring all of us to obtain some EPA permit will fix anything. People need education not a tax.