You have mentioned the two ways to get from Chania to Santorini.
You could book an Aegean flight and fly early morning to Athens and catch a connecting flight on Aegean that goes to Santorini. We did just that once and were able to get a seat sale on both flights. It took a 6am flight from Chania and an 8am connecting flight. Aegean announced a seat sale last week. If its still on you should grab those flights right now.
Ferry is a bit more complicated. If you are traveling on a Sat or Tuesday in past years there has been a Seajet ferry from Rethymnon to Santorini. You should be able to catch the first bus to Rethymnon and a taxi to the ferry port in time to make that ferry.
You could also take the first bus from Chania to Heraklion to catch one of the 3 or 4 ferries that make the Santorini run. they depart between 8:30 and 9:30. Thats my recollection but I might be off a littler bit in the timing. Yo have two risks doing this. The as I recall the Chania bus stops in Rethymnon where you have to transfer to a second bus to Heraklion. If the first bus has a delay and you miss the connection you probably will miss the ferries. Having said that the KTEL bus system is very good and they know that there are people traveling form Chania to Heraklion for the morning ferries so their schedule is set up for that.
We always choose to travel to Heraklion the night before.
For fun here are some images of where you will be.