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Heart issues cannot be ruled out unless an echocardiogram is run by a cardiologist. I don't know if your vet just listened to the heart with a stethoscope, or you actually had a workup.
Roundworms can cause problems in the throat, so I might consider doing a round of panacur if that hasn't been done recently, considering that this is a puppy. Stool tests may or may not catch them. I'm sure they've checked for heartworm (which can also be seen on an echocardiogram).
Allergies perhaps, but doesn't seem likely to me unless you are seeing other signs. I would see an internal medicine specialist for a second opinion if this doesn't get better.
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