Hi and Welcome to YT. Sorry your puppy isn't feeling well.
IMHO: Many Yorkies are diagnosed with 'large hearts' on xray.(as was mine...he just turned 15 years in Dec.) They are small dogs and many times their hearts appear large in relation to their body size.
Cardiomyopathy in dogs | PetDoc
Many puppies have kennel cough or bronchitis... were these ruled out by your vet?