If an E Liter player is bad, you can probably use quick, unpredictable movements to get close and kill it. Just don't jump or fall from ledges when you're in its sight; that makes you extremely easy to snipe. As other people said, flanking is a good idea as well, and sometimes not inking turf on your way can help. I'm not an E Liter main, but when I use it, I do check my gamepad to find any possible flanks.
If an E Liter is good, then you need to respect it. E Liters can fire three or four shots before they need to recharge, and can only throw four burst bombs at once. They need approximately half a charge to kill with damage up, and to kill with burst bombs, they either need one direct hit and one indirect hit or three indirect hits. Additionally, if they don't charge their shot enough, they can finish you off with a burst bomb. If a good E Liter is watching you and you're alone then you need to either ink some turf around you to give you more options, or super jump out. If you have enough ink around you, you can try using your sub weapons to pressure or possibly kill the charger, or in the case of a splash wall, slowly approach. If you're having problems dealing with this weapon, you shouldn't use subs like inkmine or seeker because they won't help you. The best specials to pressure/kill chargers with are killer wail and inkzooka. The latter is much more likely to kill them. Make sure you don't miss your first inkzooka shot, otherwise it's possible for your opponents to hide behind something. If you're using a bomb rush, make sure you don't stay stationary while using it; remember that you can still ink turf and swim. Kraken can sometimes work, but burst bombs are very effective at pushing the kraken back, and the chargers will probably be on a different elevation. When you have your team with you, that's when you can pressure the e liters with main weapons, subs and specials while one of you tries to flank it.
Besides for other chargers, good weapons for dealing with the E Liter (from my experience) are jet squelchers, splattershot pros, and sometimes the tentatek splattershot, depending on the map.
For gear, you can try stacking two or three defense ups to counter the E Liter's damage up, however, they can adapt and start using fully charged shots.