I stayed on Chania and it is truly one of Greece's most loveliest towns with beautiful Venetian/Ottoman architecture, pretty waterfront and lots of shops, markets and tavernas. It served as a great base to explore the west of the island.
I took the bus to Rethymnon for a day trip and it is also very nice, smaller than Chania and more in the central part of the island on the north coast. I think either town would be worth staying in.
I did a Jeep Safari from Chania into the White Mountains and it was spectacular. Small villages, gorges, mountains, goats and a wonderful guide. I forget the name of the company but the driver, Michalis was a riot! The lunch was classic Cretan food and lots of Raki making for a wonderful time.
I stayed at Jason (Iason) Studios just off Theotokopolou Street in the Old Town, which may be the best area for accommodations. Simple, basic but clean, safe and wonderful located studio. The price for a solo traveler was 30 euros which was in Oct. 2014. Even though it was off-season Chania Town was buzzing with life, not over run but enough to enjoy yourself. I lucked out when a Raki-Making Festival was held one evening and it was a blow-out with all the Raki you could drink, Greek cheeses, roasted potatoes and peanuts, live Greek music and traditional Cretan dancers. Everything was free & it was one of the most outstanding nights I've ever had in Greece!
You could spend weeks on the island and not see it all!