I dug a little bit and according to Google's AI, "According to DC law, any vessel that is used primarily in the District of Columbia must be registered annually with the DC Boat Registration Office. This includes all watercraft, including canoes, kayaks, sailboats, and powerboats."
The key here is "used primarily in DC" According to land grants that predate the forming of our country, DC owns the river up to dry land in Virginia, which means that all boats in the marinas in Arlington and Alexandria Virginia are floating in the District of Columbia's waters and must therefore be registered in DC. That includes a few hundred stored at Daingerfield island in Alexandria Virginia. When you also count the university boathouses for rowing teams, and two kayak and canoe rental places, that gets you up into the numbers this chart claims. Plus a small fleet of rental paddle boats for the tourists in the Tidal Basin.