Well the best way to travel to Crete is by plane. Aegean Airlines usually offer the best prices especially for early booking so visit their website and get an idea.
http://www.aegeanair.com/default.aspx

Crete is a very big island and I don’t think that you would need to go to a different place during your stay, have in mind that several hours are needed to get from Agios Nikolaos to Chania (from one side to the other) so visit a different prefecture every day, rent a car and make several stops on the way or just take the bus from Heraklio, there are buses to everywhere. Visit all the beaches, go to Spinalonga the small island opposite Elounda and don’t worry, there are plenty of things to do in Crete. Now if you definitely want to visit another island the closest one is Santorini and there are ferries to and from it. Santorini is truly a magical island but you will have to stay overnight. Gavdos is also a small island which is close to Crete but I wouldn’t know any details on how to get there and the schedules since I haven’t visited it myself.

Two days are more than enough in Athens. There is plenty of time to take a tour to the Acropolis and visit Plaka, Monastiraki and Thision which are very nice locations. I am currently in Athens staying at Esperia Palace Hotel and I am happy with my choice, I made my bookings on line through the following website:
http://www.athens-greece.us/esperia-palace/

We pay 88 euros per day for a double room so I think the price is pretty good too.

Hi, Yiassas! Your info about the Parthenon makes me feel very nostalgic! When we first stayed there years ago hotel staff used to come round in the afternoon and remake the beds after the afternoon nap! And if you were there for Easter you got a little package with a card, a red Easter egg and a tsoureki. In 2007 I had to organise a room for a friend at another airotel – the Alexandros. If anyone's interested in this, it was also very nice – we had a good, reasonably priced meal there. The rooms were cheaper, too, but it was November. I don't think the location is as convenient – it's supposed to be well placed for shopping in Kolonaki, but it is a little further from the centre than the Hilton – quite near the American embassy.