This article is from the Feline Leukemia (Cats) FAQ, posted to rec.pets.cats newsgroup. Maintained by Erin Miller with numerous contributions by others.
This is a touchy subject because there is often the general feeling among vets that many breeders don't know what they are doing, and the feeling among breeders that vets don't know much about purebreds. There is probably a little bit of truth to both sides. It is true that some breeders may think they understand veterinary medicine better than they really do, and unfortunately rely on word-of-mouth advice of other breeders rather than vets (eg: "Jane Smith has been breeding for 15 years and she knows a lot so if she doesn't like this vaccine, it must be bad"). But it is also true that most vets do not deal specifically with purebred issues. There is no course in vet school called "Purebreds 101" and vets are often just as guilty as anyone in misidentifying mixed breeds as purebreds, of being too quick to diagnose a "breed specific" illness with less data than if they would if the cat were not a purebred, or of not being aware of conditions which may affect one breed more than another.
Keep in mind that some veterinarians are also breeders, or work within the CFA, TICA, ACFA (AKC for dogs) or other purebred registries, and these vets are most likely going to be more knowledgeable about conditions which are more common to certain breeds. Also remember that not all purebreds are the same, each breed is different and has its own characteristics. Just like you can't say "don't vaccinate Europeans for smallpox," because there are *many* different cultural and ethnic groups in Europe.
The immune system of purebred cats has NEVER been tested to determine if it is different than that of mixed breed cats. It is impossible to state one way or another if the purebred immune system, because of inbreeding, has any reason to adversely react to vaccines that are tested on a largely mixed-breed cat population. Some people feel there is a significant difference between the two based on antecdotal evidence and won't vaccinate for that reason, and some people feel this is nonsense.
But that doesn't answer the question because this one is going to have to be answered by you and your own gut feeling. Who do you trust more with the combined necessary knowledge of vaccines, as well as about your purebred? Talk to your breeder and see if s/he is aware of the vet literature, or is repeating word-of-mouth arguments. Many of them are well aware, many read the literature more than vets do, so don't be afraid to ask them why they hold the opinions they do. Talk to your vet and ask how familiar they are with your partiuclar breed of cat as well as purebreds in general. Get a feel for both. Keep in mind that many breeders do not vaccinate their own breeding cats because FeLV vaccines can cause miscarriages and stillbirths, or it may just be cheaper for the breeder to test their cattery every year and every cat that comes into the cattery rather than to vaccinate, especially as cats from a cattery are less likely to escape to the outside world (remember the risk/benefit assessment above). Make sure you find out exactly why the breeder does not recommend the vaccine as it may very well be that the breeder has had numerous negative experiences with the vaccine in his/her particular line of cats, and that your cat may be genetically predisposed to have a bad reaction. If this is the case, you should still discuss the matter with your vet, and it may be best not to get the vaccine.