I will take a guess that you will almost certainly find organised trips that take you to the gorge and pick you up at the other end. If you're going on a package holiday your tour company might offer it (at a rip-off cost!). Otherwise you should have no trouble finding a travel agency in the town who'll book it for you.
Chania is on the north coast, Samaria Gorge is in the south of the island. To get there will mean going over the mountains on tortuous roads.
The only experience I can relate, from 2010, is that I was on a small ferry from Gavdos island to Crete. It pulled into Agia Roumeli port which is at the south end of the gorge, where a large number of hikers boarded. The boat then continued eastwards to its destination of Hora Sfakion where everyone disembarked and coaches were waiting for the walkers.
I'll post a picture of the southern end later, when I have more time.