The Palace of Minos at Knossos in Heraklion is unmissable. Much of it has been reconstructed but it does give you a better idea of the true scale of some of the ruins once you've seen how the ground level ruins can be translated into full scale buildings. I think I agree with the advice that it's best to see Knossos first for that reason. On the other hand it's a bit like saving the best for the last.
WE managed to squeeze in a trip to Knossos before flying home from Heraklion. We dropped into Knossos at 5pm for a couple of hours before going onto the airport which is about 10 kms away.
We only went to a few archeological sites in Eastern Crete and I think our favourite was the little known site of Vasiliki - just off the road to Ierapetra from Aghios Nikolaos. We had to duck through the hole in the fence to get in but other people had clearly done this aswell. It's actually older than most Minoan sites and yet in places the walls are up to head height and you can get a feel for the size of the rooms and passageways.
About 4 kms away is the bigger site of Gournia which can be easily seen from the main road.
The other palace we visited is at Kato Zakros on the far eastern coast. This is another extensive site in an interesting location albeit somewhat out of the way.
Wandering around the sites is a very thirst making experience and none of those we visited had any facilities for visitors on site ( Palace of Minos at Knossos had toilets). Go prepared for this.
The sites we visited closed at 3pm and I think open around 8.30am. It's probably best to do your visiting earlier rather than later to avoid the heat of midday.
There will be more detailed features about these sites in the tips located under the Prefecture of Lasithi. This tip is intended to give you an overview of what to expect if you visit the archeological sites.
It is a part from Phaistos (a central court of the palace), the second most important archaeological site about this ancient civilization - the best, of course, is in Knossos.
Can you imagine that there were some perfect palaces almost 4.000 years ago?
Favorite thing: The Island has a long history that goes back to the Neolithic times. It is however known for the Minoan civilization the flourished from 2600 to 1100 B.C. The island is full of relics of the Minoan ages the most famous being the palaces at Knossos and Phaestos.