The ferry is the obvious answer. Where do you want to go in Crete. The ferries go from Santorini to Heraklion Crete in the late afternoon arriving between 6:30 and 7:30. That means you essentially lose a day doing that ferry hop and if Heraklion isn't where you want to spend your time in Crete you still have a commute to wherever you want to end up. On Sat and Tuesday Seajets have a run to Rethymnon if thats closer to where you want to end up.
Here is a good ferry schedule site.
If you want to go to Chania then there may be sense in looking at an early morning flight to Athens and immediately connect to a flight to Chania (or Heraklion for that matter.) Since you didn't tell us what date you are planning on hopping I had to randomly choose a date May 7th. If you take the 6:30 am flight Santorini to Athens and catch the earliest connecting flight to Chania you will be in Chania by 8:30 in the morning. Cost just under 240 euros for two passengers. Thats probably twice the price of the ferry but you need to ask yourself is it worth 120 euros to be in Chania at 8:30 am versus 11:30 PM using the ferry system. We have discovered that time is the precious commodity while island hopping.