Hi Eric, we are a Canadian/British couple who plan to move to Crete after my husband retires in the next year or two. We have four cats, so are also quite concerned about Greek regulations etc. I found this URL to an online retail source for bilingual copies of the Pet Immigration Forms, Import Applications and entry instructions for most countries including Greece: http://www.pettravel.com/
You will certainly need the Immigration Form - EU Form 998 Greece
which is for sale on that site....(hope link works!) as well as lots of info on moving your pets.
We are lucky to have a veterinarian who has been thru the process before, and has promised to help us. Maybe your local vet can offer some assistance in the planning process. About 6 months before the move, we plan to visit the Greek Consulate here in Vancouver and make sure we have our ducks in a row. I do know that timing is crucial for some of the shots.
My best friend lives in Crete and has a big, beautiful labrador retriever. He is the second one she has had, because the first one died of poisoning when it was quite young. It was a horrible experience, and she learned to be very protective of her dog. He is never unattended when outside, and not allowed to eat anything he finds lying around on walks. Like your dogs, he always sleeps indoors. He is the happiest dog I've ever known and loves the extra attention. I'm sure your dogs will be fine. Hope I can say the same for our cat family! I have nightmares about getting them over there, and have researched the various airlines and their reputations for animal care enroute. So far, it seems that Lufthansa Air Freight is by far the superior choice. But I don't know whether they would get us as far as Heraklion, or even Athens. Lots more research to do.
Anyhow, good luck! Crete is just a wonderful place, and we are looking forward to living there, too.
p.s. Do you have any great suggestions for private health care insurance over there? In Canada we don't need it, so this is all new territory for us.