I don’t think the focusing optics will have much fun at sea, or on something that vibrates as much as a helo.

I’d put my money on diode lasers, rather than FELs, for platforms as small as ships. You don’t need to tune it too much – just pick a frequency that propagates fairly well (there aren’t too many to choose from for this kind of work, in this environment), and some frequencies are atmospherically self-tuning to an extent.

You’ll be looking at achieving thermal kills against soft targets that don’t move too erratically for a long time before drilling hard kills are possible (where you’ll have to pulse the beam, realistically).

[Too much time spent researching SFnal weapons, when I should have been keeping up with my ships, planes, missiles and guns.:)]