Julie, it would also be helpful if you'd share where you're coming from ... it DOES make a difference in your options, depending on whether you're in NY or the Northeast, or whether you're from the West Coast, because of airlines involved. Not knowing I can't advise on that, but I certainly suggest you try if possible to get an "open-Jaw" ticket flying In to Rome, and back from ATHENS. This will eliminate wasted time in back-tracking. I'm guessing that your brother-in-law will be taking the lion's share of your 2 weeks, so 5 days will be all you have for Crete, thus you cannot waste one single precious hour in transit!
If you succeed in booking such, then you can complete the circuit and again, avoid time-wasting transit by (ideally) finding a flight direct from Italy to Crete... and (again ideally) a flight not to Heraklion (central-East) but to Chania (Western Crete). If Heraklion is the only choice, then you would consider renting a car, and driving on the Very Scenic and modern highway all along the North coastline (just 2 hours) . At the end of your stay, you can fly from Chania airport to ATH airport; there are several daily flights. I would suggest rather than have a nail-biter that lands shortly before your homebound flight, you get a 6pm flight the night before, stay at a little charmer of a B & B (St. Thomas B & B) 15 minutes from the airport.
Next: where to stay in Crete?? There are good beaches on either side of the island, but the area east of Heraklion, sadly, has been overwhelmed by purpose-built concrete "holiday houses" for the UK package-tourism crowd. You don't want that scene. Chania in the West has great charm and history, and is the loveliest Old Town in Crete. And just West of town ... literally 15 minutes away... is the perfect place for you. Hotel Ammos -- http://www.ammoshotel.com -- is 5-star lovely withOUT 5* prices. Directly on beach, with pool as well (a combo rare in the area), a noted Cretan cuisine, wonderful service, absolute RAVE reviews from Trip Advisor etc. Only bad new: just 30 rooms so very hard to book. Sometimes people reserve a year ahead. Good luck on this! ... and if you cannot get in, another excellent choice in nearby location is http://www.corinna.gr -- This is bigger, and buildings surround it, but also right on beach, with pools.
The advantage of both these is that, on the landward side of the hotel, is the local road leading to Chania, served by a local bus route. In fact, if you fly in to CHania and book either of these, you would not need a car for your full stay, just if you want one for a day of exploring, a drive down the rim of a crevasse, or to mountain scenery. Chania itself is fascinating, tiny winding lanes, Venetian architecture (golden stone, terracotta roofs), delicious foods, scenic harbor sunsets.
Your key elements in this order would be (1) Booking "open-Jaw" flights (2) Determining Crete time and booking flights to/from (3) securing on-beach hotel. You need to lock these in ASAP... then you can think about "seeing the true culture."