I guess that depends on how you feel about the weather. If a misty, cool day would ruin your trip, don't go. If you could enjoy the trip whether it was sunny and warm or cool and misty, then do it.

We travelled to Ha long Bay in January 2006. (same thing as you, two day/1 night trip from Hanoi). We did not find the weather bad at all. It was misty, but we found this added to the atmosphere rather than hindered it. It was a bit cool, but nothing a light jacket wouldnt fix.
(Note though, that we had never been before/since so had no comparison to make).

I would definitely go if I were you - it is beautiful and peaceful and the rocks are just amazing. Dont let the weather put you off.

TIP: if you go, I would recommend that you invest in in a cheap $2 satin/silk sleeping bag that you can buy from any vietnamese market. On our boat (which was similiar to all the hundreds of other junkets that went out), I am pretty sure the blankets had not been washed for a VERY long time, and there was no under sheet either (just a blanket and mattress). Kind of nasty.

We went to Halong Bay as a day trip from Hanoi last December. It was lovely during the day (could wear short sleeves after the early mist burned off). It is definitely possible to return to Hanoi at night to stay in your hotel there if the overnight does not sound appealing (we had a lovely day on Halong Bay and were back in Hanoi in time for a late supper).

Cookiescampanion, which junk boat were you on at HaLong Bay? We are on the Ginger in January, 2008.

My wife and I were in Halong Bay in January 2002 and found the weather comfortable, especially with a light windbreaker jacket. We went for two nights, the first night we slept on the boat, the second night in a hotel in CatBa. For details and photos see the "Indochina" section of Our Travel Journals: www.evcal.org

msheinberg,
please post a trip report when you return. we are also considering the ginger for june 2008. I would not want to take it if i am going to need a silk sleep sack!

MSheinberg - sorry, I can not remember. It was a pretty last minute thing for us - we booked it through our hotel. We paid about $30US per person I believe. We nicknamed it the 'dodge brothers boat'.