By "recovery" I assume you meant QD right? Calling aether a recovery is pretty generous
If you sweetspot QD to the ledge, you won't trigger the hitbox, so someone standing on stage won't hit you with a counter. You can also QD short--so you enter freefall before you get the ledge, but then snap ledge because of your forward momentum. This will avoid any hitbox at all, so even if your opponent jumps down to counter you, you won't hit them. Then it becomes a bit of a 50-50 because if they know you will QD short, they can charge an attack at the ledge and punish you for having no hitbox.
In any case, save your jump and try to recover high. Try to aim for a platform around the autocancel height, but depending on teh opponent's position you can sometimes get away with a really high release and freefall to the opposite side of the stage. Even if you get hit, since you still have your jump and are now high/over the center of the stage, you should be fine to drift back and jump/airdodge back to stage.
If you have to use aether, you should consider your stock forfeit. A good player of any character (counter or not) should be able to end Ike's stock at 0% if Ike has to use aether. That said, even the best make mistakes, and if someone fails to punish aether, they eat a lot of damage. Counter is a virtually risk free way to punish aether, but you can mix it up by:
1. recovering early, so your super armor takes the counter and you hit them on the way down
2. trying to sweetspot the ledge. Depending on the character you may be able to recover low enough to avoid the counter hitbox
3. recover in reverse. This can sometimes throw off the player's timing so they get hit by aether on the way down, or if you do get hit, you will be launched toward the center of the stage.
All in all, counter is a virtually risk-free way to punish aether, but there are some mixups available. If you watch a high level Ike ditto you'll probably see them using Dair instead of counter, because there is no way to mixup aether to avoid a spike.