You know, this has probablly come up before, but I'll answer this here. I never considered 'boats a real threat. Usually when I get missile warning I just ducked behind some cover and let mountains and/or structures take most of the hits, not much you can do about a multiple AC/20 'mech other than to stay down range or simply aim for the locations where those AC's are at and hope you take them out before they're in range, after all, there are only 4 places they can be. Arms or RT/LT torse.. so just destroy those first.

. You've only got so much ammo on a Missile/Gun boat and of course, they're usually big, slow 'mechs. I prefer mobility, hard to hit a fast moving target with missiles especially when itss shooting PPCs/Lasers/ and or a Gauss Rifle at you.. or, if you get close enough, fast enough, AC/20's
Energy Boats are Silly and Overheat too quickly, even in MW4, a Energy Boat quickly overheats.. A Nova or Supernova for example, Do Lots of Damage in one volley, then you hear "Warning! Heat Critical, Shut Down Imminent, Shutting Down" And then hear fire all around you and know its directed at you while you frantically override the shutdown and power back up. (They are effective in an Arctic Area though where the ambient temperature acts as extra heatsinks, but how often are you really going to figh under arctic conditions?)
Personally I prefer a variety of weapons so I can multi-task.