I'll be flying to Greece this October (as I usually do) with Delta. October is my favorite time for Greece since it's off-season, the weather is still good, the Aegean is still warm from the summer heat and prices for accommodations are low, not to mention far less tourists . . . UNLESS you are going to Santorini/Mykonos.
Why pick the two most popular, heavily touristed and expensive of the Greek Islands even in late Sept.-early Oct.? There are numerous other islands that may provide you a more Greek Experience.
However, if you have your heart set on those two islands then do your research on where to stay, what to spend and what to expect when the cruise ship tourists "attack" the islands.
If you can fly to an island then that may be the best way to save on time but there are numerous ferries available.
Most experienced travelers do their own booking and deal directly with accommodations which may get you better service and price. Nothing wrong with an agent but you may be limited on what you get.
Regardless of whether you book with an agency or do-it-yourself you are going to have to transfer from Athens to an island and back. Yes, the agency can make it easier but you'll spend more money.
I find doing my own booking an educational experience, fun and a great way to get to know accommodation's owners.
As far as an itinerary, Athens deserves at least 2 with 3 days being better. Most will say save Athens for your return home or get back to Athens at least 1 day before your flight home in case of any delays.
I would limit islands to two with Naxos a favorite but their are numerous other islands to consider. Just make sure any island combinations are on the same ferry line.
When you say "we travel fairly heavy" I assume you are taking a lot of luggage with you. Don't! Travel light . . . you don't need to bring stuff that you probably won't need in Greece. Dress is casual for most of the country even going out to eat. Limit your luggage to the necessities. If you need something get it in Greece.
