Hand me my pistol
These hulking great beasties seem pretty daunting at first, trying to blow you to kingdom come with their fuel rod guns. But they're lousy shots, and with a pistol they're easily killed with a single shot to the orange flesh. If he's close, quickly move in to tempt him into a swipe. Then simply step back and shoot him in his orange fleshy front when nicely exposed in mid swing. Stay calm and get the timing right, and it's practically effortless. Alternatively you could sidestep and shoot him in the back. That takes a bit more skill, but perhaps you enjoy the challenge. It's also possible to pick out patches of orange flesh when a Hunter is running along in rage mode.
Actually, you can take down a Hunter with a pistol even when he's crouched in defence mode. Just pile shots in where areas of orange flesh are temporarily protected by his posture (I usually go for the eyes). As he moves or gets knocked about, tiny slivers of flesh are briefly exposed; so it's a case of crossing your fingers that a bullet happens to hit one at just the right time. Try it and see. Be aggressive and often he'll go down within a few dozen shots.
If you don't have a pistol, it's possible to wear down a Hunter with other weapons, always focusing your fire on the orange flesh. In fact, it can be a fun challenge to do so at close range. I like to use a matador style: dodge a swipe then turn to drill him with an AR or plasma weapon, or most spectacular of all, an explosive stream of needles (you'll have to be quick for that). Repeat as necessary. You could also tag him with a plasma grenade as he swipes.
A sniper rifle will do the same job as a pistol of course, but from much further away. If you can't see his fleshy midriff, you can potentially get him with a shot to the narrow slit for the eyes. Alternatively, bounce several sniper bullets off his head or his blue armour in general; they seem to have a cumulative effect.
And then there's the rocket launcher. It's hardly necessary, but if you've got rockets to spare, why not let him have one square in the chest? Very satisfying.
Whack him up good
As long as you're a confident dodger, you can also whack a Hunter to death. It'll take several whacks, but it's a nice challenge (more difficult if you're coping with two at once, but still quite manageable). Bear in mind that you don't have to wait until he swipes, and then dodge and whack him on the side or back. As long as you judge your movements well, you can keep whacking him non-stop and at any angle, including face on as he's coming towards you. Even on Legendary this will bring down a Hunter in seconds; a skill worth learning.
Over the edge
If you're feeling cocky, a stylish way of dispatching a Hunter is to lead him to the edge of a big drop then dodge a swipe to make him plummet over the edge. Mind you, it doesn't look quite so stylish if you misjudge his swipe and get knocked off yourself! See Hunter leading for advice on leading a Hunter to where you want him.
Strong or weak
Despite a lack of visual difference, there actually seems to be two types of Hunter, which I just call 'strong' or 'weak', the former being a lot tougher. On Heroic for example, a strong Hunter takes about 11 whacks to kill, but a weak one only 7, and you'll usually (or always?) find that each Hunter pair comprises one of each type. On Normal or Easy however, strong Hunters are rarer than weak ones; you'll often get a pair of weak ones. On Legendary, most or all Hunters seem to be strong, taking about 13 whacks to kill.
This is all something I took a long time to really notice; see my HBO forum post about it. Of course, a single pistol shot to the orange flesh kills any Hunter, so in that case it makes no difference what type you're up against. It only matters when you're trying to wear them down with other forms of damage.