There's a line of 'finders out there that are designed to clamp to the gunwale of a canoe or jonboat. The transducer is mounted on the bottom of a piece of PVC pipe, or some similar-looking structure. I haven't heard any feedback on those in particular, but it stands to reason that their performance should be about the same as the same head unit in a conventional application -- it's the same transducer and the same head, just held in place differently. As long as the transducer is in the water and not bouncing on top of the waves, it shouldn't make much difference.
Having said that, you could homebrew pretty much any of 'em into a portable application as well. One of the mfr's makes a transducer on a suction cup. If your jonboat's hull is magnetic (or you can epoxy a steel plate to the transom) you could perhaps mount the skimmer transducer (included standard on most low-end 'finders) with a rare-earth magnet, I'd trust that before a suction cup. Or you could mount it to a piece of 1x4 and use a spring clamp to clamp it to the transom.
Run another pair of fused leads out of your battery box and you can put the head unit wherever you want it - another magnet, another spring clamp, another suction cup... a sandbag, or just let it rest on the seat or the floor... whatever you want...
If you don't already have a battery on your jonboat, you can get an AGM or gelled-lead-acid battery at Batteries Plus or lots of hobby shops -- the RC industry has really made those batteries easy to get to. You'll need 12 volts, then it's a question of how many amp-hours you want. I use 5, and it'll run for several days without a recharge. You can waterproof the battery by putting it in a watertight food-storage container from the kitchen aisle at walmart, and don't forget to fuse the leads. The expensive part is a charger. If your kid's already got a battery-powered jeep that uses 12v, use that charger. If not, you could adjust the float voltage on a motorcycle trickle-charger, but I just shelled out the $25-$30 for a smart charger to match the battery.
Hope it helps