Most people going to Halong bay do so on a small package trip that you can arrange easily from anywhere in Hanoi.
Typically it includes transportation from Hanoi to Hai Phong where you board a junk style boat that sleeps maybe 20.
The boat takes you out through all the islands and in our case we spent one night on the boat with meals included,
then they put us up in a hotel for another night on Cat Ba Island. We saw a few of the sights on Cat Ba and then the boat takes
you back to Ha Phong and bus back to Hanoi. All meals were included plus the hotel on Cat ba.
Was pretty nice trip and fairly reasonable. The first time we went was in 2001.
We went back in 2005 and were amazed at how many more boats and tourists were there than the first trip.
Photography-wise it was an amazing place though often there is that typical white hazy sky of Southeast asia.
You can check out some of my images from those trips here
http://www.msphoto.ca/Vietnam_slideshow.html