G'day,
Your concerns are understandable. When I first investigated Halong Bay cruises, I had my suspicions. But I had read advice that booking through a travel agency was the recommended option as opposed to the tour operator. I think this is where you may have run into difficulty. The agent has access to all the tour operators and will liaise with them on your behalf. I took me a while to figure this out but I can fully recommend halongcruises.net
Email Andy at sales@halongcruises.net and he'll sort you out. I just came back from a trip to Hanoi and Halong Bay just last week with my gf and we couldn't have asked for a better cruise. Andy sorted everything out for me and answered my incessant questions prior to booking. He has perfect English and is prompt with responses. The tour operator he booked us with for 2days-1night was Halong Phoenix Cruiser. I can also recommend their services and the Phoenix Luxury boat in particular as this is a relatively new boat. The double room especially, though small, was quite impressive. Everything was included, transport from Hanoi, food, life jackets, they even handle our luggage.
I'll also take this opportunity to raise another point for other would-be travellers. As I mentioned I took a 2day-1night cruise. Really it's half a day followed by another half a day with one night on the stationary boat. As other ppl have noted, the drive there on a mini-bus takes 4 hrs from Hanoi. I was wondering why this is, as for most of us, 170km only takes about 2hrs. The road there is not a highway and the speed limits are slow, plus the traffic and one toilet stop. There is plenty of countryside scenery however. So you get there around midday, you go straight onto the boat. The next day the boat will come back to the wharf also around midday and the bus will take you back to your hotel.
For those who just want to see the limestone karst formations, despite what others may say, a one day cruise should suffice if you don't mind travelling for 8hrs on a bus in one day. I recommend the cruise I did 2/1 if you want to take in the scenery a bit more. Really, once you've seen a few limestone mountains you've seen them all. The longer cruises 3/2 or 4/3 are really for those types of travellers who like a bit more relaxation and luxury or want to do more activities and see more sights, like caves, beaches, islands, floating fishing villages etc.
Hope that helps.