At the risk of stating the obvious, if you go via Albania you'll pass through Montenegro as well as Albania before Croatia ... which could be very enjoyable, but seems like a very different trip from your initial idea. If you want to spend some time visiting those two other countries then go for it - but if you are just looking for transport to Croatia there are probably easier ways. Many of the most interesting sights in Albania are south of Tirana, the "wrong" direction if you arrive at Durres and want to head to Montenegro. Following the coast north via Shkodra-Ulcinj-Budva-Kotor-Dubrovnik is fairly straightforward with lots to see on the way, but there are only a couple of minibuses a day across the Albania/Montenegro border, and in January possibly only a couple of buses a day
I'm not sure if your question about ferries is only about getting to Croatia or getting around once you are there. For getting there, http://www.jadrolinija.hr/ shows the timetable for Ancona-Split and Bari-Dubrovnik up to December 2008, January 2009 is likely to be similar (although not guaranteed of course). For domestic ferries, as dlmtn said, the main islands are inhabited with permanent populations so ferries still run for those people who live there. Not as many as in tourist season, but enough to visit places like Korcula or Hvar with no real difficulty. Buses and trains run normally.
Sunset in Zagreb on 1st Jan is at 16.22 - for me that's the most frustrating aspect of midwinter travel, not so much the weather but the limited daylight hours for outdoor sightseeing. Of course that's not specific to Croatia.

