There's a large amount of different methods of killing Fontaine. A method of dealing damage to him that will always work is finding an explosive item that can be picked up (I.E a gas bottle), sticking a few proximity mines to it and using telekinesis to throw the bottle at him. Aside from that, just make good use of your plasmids (particularly Electro Bolt, Incinerate and Winter Blast) and you should be fine.