What we have here is:
DC-DC converter from ~12v to 5v. Another DC-DC in the IPad charging the battery. Modern DC-DC have gone up a lot in frequency to minimise loss and size. Also to get the frequencies away from AM radio frequencies. Right up to the frequencies used for aircraft comms. Also remember aircraft comms is also AM. Things are not going well here. Now we want to place the USB charger right next to the radio, along with the IPad. Also prop close to the antenna. Things are getting worse, not better here! What to do.
1. Is it the USB charger, or the IPad. Get a long USB cable and get the IPad away from the radio and antenna. If the noise stays, it most likely the USB charger. Plenty of advise in other posts about that. But also you might consider wiring for the USB charger to be much further from the radio. If it's the IPad, you may gain from moving it away from the radio.
2.Terminate the radio cable, at the antenna, with a 50 ohm load. If you still have the noise, you have a crappy radio, or cable, or installation. You need to fix that. That probability will also fix your general radio comm problems!
3. If the problem goes away with the antenna termination, then the noise is getting into the antenna. If you can't fix the noise at the source, then consider reposting the antenna further from the cockpit.
4. I usually also advise a sacrifice to the GODS here, as most interference issues don't seem to have a rational cause. However that tends to be frowned upon these days.