Dave has provided a doable itinerary. I personally wouldn't choose that itinerary - too many buses and boats. So, here is an alternative.
I don't know much about Crete west of Domata Gorge. But, there is a nice walk from Sougia that can be done in a day from Chania. http://www.sougia.info/walk-lissos.htm
Check the June bus schedule.
The rest of the itinerary is based on the assumption that you can carry everything you will need for 1-2 weeks down the Samaria Gorge. You don't need sleeping bags, or any camping equipment. You'll be based in villages every night.
So, bus to Omalos. Walk down the Samaria Gorge.
Stay at Aghia Roumeli for 2-3 nights. From Roumeli: a) day walk to Domata Beach and back; b) day walk up past the two western forts and as far up on Papoura as you are inclined to go. The views from there are spectacular: http://www.panoramio.com/photo/12389566
; c) day walk up the Eligas (Elighia) Gorge - at least up to the saddle above Flyskouias, possibly with a side trip up to the two eastern forts - http://www.panoramio.com/photo/3255630
; d) stay an extra night and do the walk up to the eastern forts on a day separate from the walk up to the Eligas saddle.
Walk to Loutro on the A4 - packs on the ferry. Stay 2-3 nights. From Loutro: a) day walk up the Aradhena Gorge - at least to the kalderimi past the bridge - perhaps higher up. Back through Anopolis; b) day walk through Livaniana, to the Aghios Athanasios Church, across the Aradhena gorge, up to Aghios Ioannis, down to the coast, and back on the A4; c) day walk up to Anopolis, down the ravine to Chora Sfakion, back to Loutro on the A4.
Walk to Chora Sfakion - packs on the ferry. Stay 2-3 nights. From Chora Sfakion: a) day trip, bus up to Imbros, walk down the gorge and back to Chora Sfakion; ; b) day walk up the Illingas Gorge, up the east side to Mouri, back through Kavros and down to Chora Sfakion; c) day walk up the Sfakiano Gorge to Kali Laki, back either via Imbros or Mouri / Kavros.
NOTE: Some of these walks are long and strenuous. You will probably want to add in some nights at each stop to have some rest days. Or, of course, you can just skip some of the walks. These are just ideas.