<<<I'd rather suffer the heat to be out in the open (although shaded from direct sun would be nice) rather than be inside in an airconditioned lounge looking out through windows.>>>

This would tend to be me, too, but the shade from the direct sun would be a must. Thanks all for your recs.

NeoPatrick - I don't disagree with you. I merely tried pointing out that it is nice to be able to escape from the heat after enjoying the bay. You were very fortunate to have such comfortable weather!

Bai Tho Junk is a good junk for you, it has private AC cabins,nice itinerary, delicious food, if you book with a good agent, you can have private transfer to/from Hanoi, I used Indochina Orbit agent for my last trip, sounds reasonable for me, they have very good price ($100-$130/person for such cruise with Bai Tho Junk if you are 2 persons)

I just came across this discussion because I'm looking into Halong Bay cruises for early March. Does the advice about AC depend on the time of year? Not sure when the above posters were there.
On a website for Halong Bay weather June-September are rated as causing a "high" degree of discomfort due to heat and humidity. The rest of the year, it's "medium." See http://www.vietnamclimate.net/halong-bay-city

We were at Halong Bay in May and it was incredibly hot.