don't know about day trips but I have booked on flying cat4 from heraklion on 21/5/10. I booked online months and months ago but only just got confirmation and when it arrived they could only offer business class ( 9euros extra) so obviuosly popular. maybe your tour operator, or any other for that fact, would be able to book something. the flying cat only takes 2 hours so you might get some decent time on the island.
good luck

Ali T

I wrote what I know on another thread (it's near the end)
http://www.holidaytruths.co.uk/viewtopic.php?f=10&t=141487
When we booked it was only a couple of days before & we had no problem. Though that was 30th Sept.

Given that you're a family group with children I would suspect that one of the tours might be more approriate & probably cheaper. We were travelling back via Santorini, so stayed there for a couple of days and the island is stunning in places.
However I wouldn't say it's easy to get around independently unless you use taxis or a hire car. The catamarans (well the MegaJet didn't) don't dock at the same place at the cruise boats which is where the steps, cable car & the donkeys are.

Pete