Where does your ship actually dock?

it says Halong Bay ! We are on Celebrity Millenium a big ship!

Where is the cruise going? and where has it been?
From where the junks dock in HB, it is a good three hours to Hanoi, could be even longer. Not sure what you would do hanging around Halong Bay - I assume the cruise you came in on went past the karst formations which are stunning. If not, a jaunt out into the bay to get looks at the formations would make a nice afternoon. Also depending upon the weather you could do some kayaking if that appeals to you.

OTOH if you don't mind spending 6+ hours in transit, seeing Hanoi would be worth it to me. Does the cruise ship arrange for transportation into Hanoi?

Leave leave from Singapore (2 full days to visit) w/ stops in Ko Samui, Thailand, Laechobang (port for Bankok- overnight), Saigon(Phu My), Nha Trang, Chang May (port for Hue and Danang), Halong Bay and Hong Kong.

If you have enough time to do an overnight in Hanoi, then I would go there. You can spend time just wandering the streets of the old city, soaking up the atmosphere, sampling some food, wandering around the lake which is close by the old city and the French quarters. Hanoi is fantastic.

The drive between HB and Hanoi is not very interesting. You would spend half your time getting to and from Hanoi, in order to spend, say, six hours in a town which is easily worth six days. You could hit some of the high points listed in all the guidebooks, but I suspect you'd miss the charm.

I would look into spending the day on a boat in HB. But this just illustrates the down side of cruising. It's no way to visit SEA.

I do agree with thuradaysd. The road is long and boring.