With a plain raft intercept the edge of the raft into the bird as it's swimming and it'll walk on your raft, once on the raft bola it and use your K.O. method once knocked out DO NOT MOVE THE RAFT.If you hit a bola and sinks into the water retrieve the bird and remove the bola underwater. If flying then hit it with something that doesn't do much damage then kite it over land then either bola in mid air or wait for it to land then use K.O. method.
Ever need lots of raw fish. Easy! Instead of swimming around in the water risking getting attacked by megapiranhas, simply make a saddle for your Pelagornis, Ride it into the water, and it one shots every small fish.