After you use review sites like Trip Advisor to identify some of the hotels you like best in each place, you might want to consider hiring a local travel agent to make all your reservations in a package booking. Tell them where you want to stay, but also describe in general what type of place you'd like, and see if they have alternate suggestions. They'll not only book the hotels but will also arrange for a taxi pick up from the airport, rental cars, ferry tickets, etc. The advantages are significant. It gives you a local person to contact if anything goes awry. Here's the biggie: if you've booked a hotel on one of the islands on your own but you cannot get to it that day because the ferries are down due to weather conditions or a strike (these things do happen!), you'll still have to pay for that night's stay in that hotel, and find a new place on your own. If you've booked that hotel through a local travel agent, you'll be able to contact your agent at that company, and he/she will cancel that night for you, and find a new place for you to stay in the place where you're stuck, and you won't have to pay for the hotel you couldn't get to. For our 2012 trip to Greece, we worked with Aegean Thesaurus Travel, (based on Sifnos even though we didn't stay there).
I never spoke with them by phone. After emailing the company for a proposal, and then choosing them based on their response, I was assigned an agent and all of my subsequent communications with her, to finalize all the details, were also by email. Ahead of our trip, I was in touch with our agent quite a few times with general questions, on many topics, and she always seemed happy to give advice. Her emails were always prompt and helpful.
I don't believe that we paid any extra for the hotels and other things she booked than we'd have paid if we'd booked them on our own. We didn't have her book any tours, entry tickets, etc. but I know this would have been available.
When we arrived at the airport in Athens, tired after our overnight flight, our taxi driver was holding a sign with our names on it, and on the island of Naxos, when we arrived by ferry, likewise someone was standing at the car rental area with a sign with our name on it, to personally guide us to our booked car. All of that felt very welcoming in a foreign country.
I'd never used a travel agent, before that trip, (and haven't used one since), but when planning our Greece trip, I'd read that it's a "different story" in Greece and it's smart to do so. We were very happy with our decision. I'm guessing that even if it's too early to book some of your favorite hotels on your own, a local travel agent might be able to accomplish this for you. You might want to put together a tentative itinerary, describe the kind of hotel you like (or even use actual hotel names), and email this itinerary to a couple different travel agents to see if they'd like to put together a proposal for your consideration. This is what we did, and we picked the travel agent who responded the quickest and seemed the most enthusiastic and intuitive.