Can I get a ferry boat from Bodrum, Turkey directly to Heraklion, Crete in September 2014?
No, there are no direct ferry routes for this journey you have requested.
Most ports on the Turkish coast have a corresponding port on the Greek island in the Dodecanese.
For Bodrum the Greek port opposite is Kos. You can take the Bodrum Express, services run very frequently and the journey takes around one hour. Cost is about 30 Euro.
Kos is a lovely island, Kos Town is very pretty and you can get good accommodation right on the harbour, close to where the ferries sail. Don't forget to see the big ancient tree where Hippocrates sat and taught...it is still there in a lovely square in down town Kos! If you have time you could visit the Sanctuary of Asclipius in the hills and enjoy the serenity.
You can to travel from Kos then south to Rhodes (3 hours) then a long ferry from Rhodes to Crete. This is quite an extensive journey of 14 hours. Or you can fly with Minoan Air from Rhodes to Heraklion, duration is 1 hour and cost is around 70 Euro.
An alternative is Kos to Santorini to Crete. The port you will arrive at in Crete is Heraklion.
From Kos Town the ferries depart regularly to Santorini (Thira) and the crossing takes 5 hours. Then from Santorini it is a two hour journey to Heraklion.
We can't suggest whether to enjoy Rhodes or Santorini because they are both fantastic, with loads to see and distinct characteristics. It really depends on your own personal interests and travel style.
The Medieval City of Rhodes is a UNESCO World Heritage site. It is so thoroughly restored, it feels like you are in medieval times, and when you glance up at the fortifications you expect to see an archer up on the wall.
September is only just starting to get quieter after the busy summer months of July and August, so there will still be many ferries on all of these routes. Just check your schedules to ensure you have the connections sorted out, or better still, enjoy a night or two in these beautiful Greek islands.