Fly with Turkish Airways direct if you have the budget. Book direct on their website for cheaper fares.
Take a ferry over to Bandirma and then train to Izmir. About a 8-9 hour trip, very clean and nice, and very cheap. Leaves daily at 0700 from Istanbul. It has been a while but I think it cost us about $25US each.
Or there is a bus which is also is very nice but I recommend the ferry/train option as it is well worth the views and the comfort. over 9 years ago