Tracer, Sombra and Pharah are good against Zarya. Choose depending on the comp you and your enenmy have.
With Tracer farm up your ult quickly then get her to bubble, wait a second and pop it on her bubble. Bubble makes it easy to sticky and if you wait a second the bomb will outlast the bubble. Practice it to get good timing. Or you can start shooting her to get the bubble, back off then re-engage two seconds later. Be careful of her alt fire though.
With Sombra, get high ground be sneaky and hack her. She either uses her bubble to stop it or gets hacked. Either way she gets no charge from it and you can hack her after the bubble comes off cool down. Zarya with no bubbles or charge is useless and will take a long time to get ult from. Her EMP also takes off half of Zarya's health making her an easy target.
Pharah can shoot Zarya from outside her effective range without any drop off in damage. Just be careful about feeding her charge. If you shoot near her you can bait the bubble out. Don't run it if they have a lot of hit scan though.