Four nights in Chania and three in Heraklion is a good mix. You'll enjoy both cities: the problem, as there is so much to see and do, will be choosing your day trips.
From Chania, my first choice of day trip is the one goanjock has suggested: take the first bus of the day (usually at 8.15/8.30, check nearer the time) to Chora Sfakion (known locally as Sfakia) and the 10.30 ferry to Loutro, where you can explore the peninsula on the way to Finix: a beautiful walk, the path hugging the coast in one direction, and taking you over the hill past the Turkish fort in the other, with spectacular hill and coastal views all the way. You can have lunch in Finix, or in Loutro and return to Sfakia on the 18.30 ferry to catch the bus back to Chania.
Alternatively (or additionally) since walking is one of your priorities, you might want to walk the Samaria Gorge. You can take an early bus to Omalos, at the head of the gorge, and after walking down it to Agia Roumeli, travel (as above) by ferry to Sfakia and bus back to Chania. This has the advantage, apart from the gorge, of the longer and even more exciting coastal ferry trip.
Another possibility is the Imbros Gorge - about half the length of Samaria, almost as beautiful, and less popular.
May is a good time to be in this part of the world: the spring flowers should still be plentiful, particularly in the gorges.
Other possibilities from Chania are Ancient Aptera:
http://www.chania-crete-greece.com/aptera-chania-crete.html
and the monasteries of the Akrotiri peninsula
http://www.west-crete.com/akrotiri-peninsula-crete.htm
And there is lots to see and do in Chania itself: don't miss the Venetian harbour and old town, the Archaeological Museum, the Maritime Museums for starters. You'll find loads of information about the entire area, and Chania, and the gorges, here:
http://www.west-crete.com/
That should be more than enough to get you started. :o)
Heraklion is a vibrant, lively city: it takes a little time to get to know and like it, which not many visitors give it, but it amply repays any time spent there. Of all Crete's cities, it's my favourite, combining massive, impressive Venetian structures - the city walls, the fortress, public buildings and fountains - with all the buzz of a working city with friendly people and lively street markets.
Apart from Knossos, easily visited by local bus in half an hour, there are the three ancient sites of first importance south of the city: Phaistos, Agia Triada, and Gortys. They can all be visited in a day with an organised excursion: the disadvantage of this is that you don't get enough time in Gortys, the largest of all Crete's ancient sites, and in some ways the most fascinating. If you had more time I'd suggest doing them in two separate trips, but an organised excursion may be your only option.
If that isn't enough ancient-site-wise, you can also visit the palace of Malia, and ancient Lato and Gournia.
Finally, you'll want to allow plenty of time for the Archaeological Museum of Heraklion. It has always been one of the world's great museums, but since it re-opened after its eight-year renovation it is one of the most beautiful too. It's huge, and can't really be seen properly in one visit - but you're there for three days.
I hope this is some help. Enjoy your planning, and come back with specific questions once you've roughed out a plan.
Edited: 6 years ago