I second those that suggest taking the ferry from Italy to Greece (Patras). It’s a fantastic experience and one you shouldn’t deprive yourself of. I now live in Iraklio, Crete and have taken the ferry to Greece from every port in Italy. I’d recommend leaving by ferry from Venice (since you’re there). Traveling by train to a port more south in Italy (Ancona, Bari, Brindisi) will not save you much money or time.
Minoan Lines (fastest, newer boats, more comfortable, €55 one way in low season, after August 15th) leaves daily at 14:00 and arrives at 20:00 the next day. With ANEK Lines (slowest, older boats, €50 one way in low season, after August 15th) you have more options: Mondays at 18:00, arrival at 06:00, Tuesdays and Wednesday at 19:00, arrival also at 06:00, Thursday no sailing, Fridays to Sundays at 12:00, arrival at 21:00 (you’ll be spending between 30 and 36 hours on the ferry). All ferries halt at Igoumenitsa (north of Greece) and the island of Corfu. Minoan mentions a €8 fuel surcharge per way/passenger. ANEK has no fuel surcharge but things can (and invariably will in Greece) change, so check the internet (good site is http://www.greekferries.gr).

Patras is cultural capital of Europe this year and there are bound to be lots of activities. Don’t rush out immediately but enjoy your stay there. Also see http://www.telegraph.co.uk/travel/main.jhtml?xml=/travel/2006/06/28/etpatras28.xml&sSheet=/travel/2006/06/28/ixtrvhome.html

To travel from Patras to Piraeas (where you’ll take the ferry to Crete, take the train. In Patras ask for a ticket directly to Piraeas port (port=limin or limani), it’ll cost you between €5 and €6 one way for a plain seat (comfortable enough). Buy your ticket in advance if possible (immediately when you arrive in Patras). You’ll have to change trains in Athens for Piraeas. Total trip takes about 4 hours.

1: PATRAI – ATHINA

Train No Departure Time Arrival Time
11 05:55 09:28
21 09:55 13:28
23 13:55 17:28
25 15:54 19:28
25 15:54 19:28
27 17:57 21:28

2: ATHINA – PEIRAIAS LIMIN

Train No Departure Time Arrival Time
1531 06:40 07:01
1535 07:45 08:06
1537 08:16 08:37
1539 08:46 09:10
41 11:07 11:36
47 11:07 11:36
51 11:37 12:07
1549 13:46 14:07
53 15:16 15:49
1553 15:52 16:14
71 16:43 17:11
1559 17:46 18:07
2531 18:48 19:11
55 19:46 20:14
2535 20:46 21:09
57 23:09 23:37

I’m sorry but I can’t seem to get the formatting of this table right: there are 3 element, first the train number, then departure time, followed by arrival time. I hope you can still figure it out. You can find all this information on the site of OSE (Organismos Sidirodromon Ellados): http://www.ose.gr (click ‘EN’ for English).

The last stretch (you’re almost there!) takes you from Piraeas to either Chania (in the west) or Iraklio (more central) of Crete. Again, you have the choice between Minoan and ANEK. You could ask in Venice for a combined ticket, that might entitle you to a discount if you travel both legs with the same company (not 100% sure about that though, these rules change as often as the wind here).

Piraeas-Iraklio: departures 21:00, arrival 06:00, €37 Deck one way with Minoan, €32 with ANEK. Again, the Minoan ferry is newer and a bit more comfortable than ANEK’s.

Piraeas-Chania:
With Hellenic Seaways (high-speed catamaran), departure at 16:00, arrival at 20:45. €41.50 economy non smoking.
With ANEK, departure at 21:00, arrival at 06:00 next day. €30 deck one way.

About sleeping on the ferries: do what everybody else does and install yourself in a quiet corner. Do this beforehand, mark your territory with a folded out sleeping bag or something that can serve the same purpose! Don’t be too shy about this, if it is crowded, you’ll need to be firm. Some people take up whole stretches of seats in the bar e.g. Then have a few glasses of red wine before retreating and Kali-nichta (good night)!

Enjoy Crete, the nicest place on earth, chosen by the gods (and by me, since I chose to live here :-)