How far are you going to haul this boat? If you plan to try this on public roads, you may have a problem, as most boat trailers are licensed vehicles and obviously your bike is not. It may be seen as a road hazard, no different than if you were to use a farm tractor to haul a trailer on public roads; it is generally not legal to do.
If you are talking about a folding kayak, that should be no problem as the size and volume of a packed boat is small enough to haul on a typical bike trailer.
That completely ignores the issue of your being able to control the trailer with a bike pulling the boat on the trailer. Tongue weight issues aside, there are also sidewind forces, braking, lighting (most states require brake light wiring through the rear of the trailer). It is basically a terrible idea.