i have driven with boats, carried them on planes and send them via cargo...
overall, there's no fixed rule with the airlines and the rule of just showing up and hoping for a helpful check in (lady) still counts.
as mentioned, they don't ask for bags but (nowadays) for money and this usually is negotiable.
if it's a charter you will get away better, also (usually) the cheaper/smaller airlines will let you get away with it. standard airlines (qatar, lufthansa, BA, Thai, IA, Aeroflot, RNA) all charged money which varied from a whooping 380$ to a bearable 30$.
Best is to ask (before you buy the ticket) if it is possible to get a fixed charge (lufthansa does so for 100$ both ways).
all the rest is open to the gods, the desk lady, the size of your boat, the size of lef luggage compartment in the plane and and and...
so there' s nothing really fixed to say but best is to get some direct inquiries from the airlines you might want to fly with and then bargain...
as mentioned, there are airlines/destinations which wont give you hassle (at least on way but who knows about your way back..

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www.shivaoutdoors.com/boathousenepal (no infos of flying but of destinations/rivers/trips)