There are so many property developers and builders 'producing' new houses that it is easy to shop around, online or whilst in Crete and possibly find what you are looking for with the minimum of fuss and time. Take time to look around and compare prices between different estate agents. Properties are rarely sold exclusively through one agent and prices can vary a lot for the same house from one estate agent to the next.
At the time of writing (2014) your most cost effective option if you want to buy a property in Crete is to buy one that is being resold. After the building boom of the last decade many (especially foreign, a lot of them British) owners decided that Crete wasn't for them after all. But the Greek crisis and the uncertainty that went with it have brought the property market to a standstill and many owners are now desperate to sell and prepared to offer very good prices. It is totally a buyer's market and if you find a property that you like you should be able to buy it quite a lot cheaper than it would cost you to build it. And of course you see what you are getting and save yourself a lot of (potential) hassle.
Whilst this is far more romantic than buying a new ready-made house it will likely cost you more and is possibly very hard to control unless you already live in Crete. If you go that route, make sure and double sure that you have a capable and reliable architect who can supervise the project and keep you well informed of the progress. I would still say that this type of property is best left to those who live on the island or don't mind traveling to Crete often to keep a close control on what is going on. The renovation of an old house is not as predictable as building a new one so you will invariably hit some snags and costs overuns.
Choosing the right plot of land and buiding your house on it is
the most flexible of all options but with the same drawbacks as above:
do you have a capable and reliable builder and architect who will
make sure that things go according to plans and time scale in your
absence? Here again, I would recommend this option to people living
on Crete but not necessarily to those who only visit occasionally.
If you choose to go down this route without living here, at least take the time to get some recommendations from others as to the reliability of the people you will be using.