We want to travel via ferry or flight from Crete to Bodrum or Izmir, Turkey. We will be traveling in Sept/October? What is the best way to do that in a short amount of time?
You cannot get to Izmir from Crete by ferry, only from Bodrum by bus or plane.
Crete>Bodrum ferry schedules: http://www.feribot.net/feribot/?lang=en
You could get an internal Greek flight from Crete to Kos (or get a ferry), and then get a ferry from Kos to Bodrum.
Sky Express offers flights from Heraklion to Kos non-stop.