With the information you've given it would be hard to give a best answer but here are some thoughts.
While a trailer would be your best bet, if you're on a small boat most trailers, even disassembled, are going to more or less double the space required to store your onshore transport. If you're handy you might consider designing and building a small trailer, say with 8" or so wheels, just big enough to haul the containers you mentioned. Such a trailer could be disassembled into the size of a breadbox. In fact, you could take the wheels off and use the rack to secure the jerrycan/jug/whatever inside your boat. Little space consumed then. Probably market the things on ebay to boat owners, then buy yourself a yacht and leave the hauling chores to the crew.
On to your original question about using a rack: 5 gallons of water is around 40 lbs, a pretty heavy object with a small footprint. I've transported a 5 gallon jug of water on a rack myself. The distance was only about a quarter mile (in a campground) but it turned out to be a bit tricky. When the water sloshed around it imbalanced the load, considerably and almost unpredictably. If you do use a rack make sure you fill the container as full as possible to minimize sloshing. Additionally, that 40 lbs is too heavy for most inexpensive alloy racks, so you may need an 'expedition' or cargo quality rack, which may be nearly as expensive as a cheap trailer. Since you mentioned Dahons, I happen to know the steel racks Dahon puts on its entry level bikes like the Speed D7 are very sturdy and may be able to handle a load like that (but I'm not certain of their exact weight limit). The top of those racks is smaller than a standard rack. But if you're (again) handy, an extension frame of aluminum angle stock custom built to carry the can/jug/whatever could be added to such a rack.
Finally, whether you end up using a rack or a trailer, I'd be wary of using bungees to lash down that type of load. Rope takes more work but doesn't stretch should the load shift quickly. And I assume you're carrying fuel in the jerrycan, so any spill on the side of the container may eventually weaken the elastic in a bungee. I believe they make mooring lines out of some type of fuel-proof nylon or polyester, might consider using that.
There is a Utility Cycling subforum here, you can probably get more ideas there.