I hear a great deal about this. It's because of caving circles that I actually know about the existence of the museum. Friends work at the museum, and conduct research in its name.
I was not too sure what to expect from this natural history museum - I have not really been to one since childhood. The end result was a slight disappointment, brought about essentially by higher expectations than is proper. Perhaps I need to sit and think about what a natural history museum is for. The fact that this one is attached to the MiniEdu rather than the MiniCult may be a bit of a hint, but the whole "what is a museum for?" discussion can wait for another day.
The Heraklion Natural History Museum is divided into 4-5 sections: the dioramas make up the bulk of two floors, the temporary exhibition (currently housing the Antikythera mechanism exhibition), the living gallery with live animals, the earthquake simulator and an external space for traveling exhibitions (currently housing a medicinal plants from across Europe exhibit). The museum costs €6 and has a pretty good bookshop (even though it does not accept credit cards!).
So: Dioramas: The museum has set up dioramas of stuffed animals and vegetation from a number of habitats (mountain, plain, lowland) from a range of places such as the Balkans, Cyprus, Libya and Crete itself, in an attempt to show how the flora and fauna changes from zone to zone and from place to place. All well and good. My favorite question remains unanswered, and it is not asked nor even hinted at: why? Why do we have goat-like animals as the main herbivores and birds of prey and whatnot in each of these dioramas, but in each one they are slightly different? Why is it different eagles and different goats in each one?
The opportunity to discuss foodwebs and (in this, the year of biodiversity and Darwin's 200 years) Evolution has been missed. So, yes, one disappointment there.
The live animal zone was interesting enough although my eco-instinct kicks in and I get all anti-zoo whenever I see animals kept in small boxes. It's hard to balance the benefits of seeing a live viper (οχιά) against the ethics of having seen one in a small box dressed to look like the natural environment. This is most disturbing in the terrapin tank where all the little guys are falling over eachother, literally, in their attempt to get to the best spot under the lamp illuminating their exhibit, which, presumably is also a welcome heat source for the cold blooded anapsids.
Finally, on to the earthquake simulator: The simulator is very popular with the locals. It has been on local TV and subsequently on youtube and the lady giving out the tickets as you enter will suggest that you don't miss it and tells you the time of the next performance. I have been on the simulator at the British Museum of Natural History (Science) as a child and I have felt "the big one" of San Francisco (1906), so I was thinking, like, what's the point? I skipped the simulator.
I regretted this the moment I heard and saw the kids in the simulator screaming (with terror or with glee, I know not) as they were rocked to the rhythm of the Kobe earthquake of 6.9 Richter (1992). wow. So, perhaps worth not missing after all.
In all, the museum is great for the city, albeit a little overpriced, especially to someone used to getting into MiniCult museums for free. I am probably wrong in mentally comparing it with London or even the Goulandris in Athens. Speaking of which: where are the insects, the butterflies and the invertebrate endemics of Crete? Kids love to look at the creepy crawlies and Crete has plenty. I will assume that the curators have this in mind.
To summarise, a good museum for Heraklion which can with time and effort become a great museum for Greece.
The Natural History Museum of Heraklion - already a happy gem for the island of Crete, potentially a gem for all Greece. 
Left: a view over the dioramas which take up two floors of the museum. Right: An inhabitant of the live gallery, a Viper - Οχιά. Ethics of keeping live animals aside, an opportunity to get to know one of the poisonous snakes of Greece, close up!
Left, a Cypriot mountain goat (as per the country's Euro coinage), center a Cretan wildcat and right Bonelli's eagle, all from the various dioramas on show.
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