Axe, BB, ES, WW, Ember... They all counter Meepo as long as you damage all the meepos in an AOE burst.
Axe: Well he's a tank. Q on all meepos, Blademail and spin between them.
BB: Well he's a tank too. Sit between them, spam W and since you're a tank and barely feel anything from your sides and back and also keep throwing quills from damage threshold, besides the damage from ult. And that's it.
ES: Well obviously blinking between all of them (or just go there) and ult will be a great echo counter since they'll die easily.
WW: Get grabbed by his Q and hit E, then all meepos come and you don't feel anything. Then ult a clone and he'll die.
Ember: W every 6 seconds, they'll die and you won't be even hit since you ult back to somewhere he can't reach you.
Well hey, 5 heroes I just mentioned, that's a nice team to use.
Unless you want to change ES to Sand King or some ranged carry if Ember wasn't enough for you.
Oh right, Sand King is also a counter for meepo (well not much but he's something).