Wheres the best way to book this?
I'd book with the carrier. The two biggest ones are Minoan (minoan.gr) and Anek (anek.gr). An overview of all lines can be found on several booking portals such as goferry, isferry etc.
Depending on the day, Blue Star Ferries also offers an overnight to Athens/Piraeus. https://www.ferryhopper.com/en
What type of seat are you looking for?
Do you want a berth?
It's a long ferry ride depending on what ferry you take.
A regular seat will be the least expensive but not the most comfortable and it's first-come-first-serve. A "airplane" seat will be more comfortable but more expensive and you can reserve it.
A birth will be the most expensive.
An option for the ferry is a flight. Very quick but pricey depending on which airport you arrive at.