Which floating villages/markets in Cambodia/Vietnam are most suitable for a touring family with small children in February?

I can only offer information (from 2014) about the floating village of Prek Toal, at the mouth of the Sangkae river (into the Tonle Sap). I found it absolutely fascinating to see how these people live in floating houses and even raise animals and small gardens floating on the water. Tourism doesn't seem to be a big factor there yet. I am certain kids would love it.

There is a connection by boat between Siem Reap and Battambang, which passes through Prek Toal and is altogether a stunning experience. But it is also very long, hot and crowded, and will be worse so in February when the water level is lowest. I cannot recommend it at that time or with small kids. Otherwise you could have yourself be picked up in Prek Toal after getting a guided tour there and maybe staying overnight (depends on how the times line up).

From what I've heard, the boat transfer between Siem Reap and Phnom Penh is optimized for speed, not for sightseeing, but I'm not sure. Maybe there is one that stops at a floating village where you could do the same combination described above.

I can recommend Kampong Phluk Floating Village on the lake Tonle Sap. This is possibly the easiest to reach from the city of Siem Reap: it takes less than one hour by scooter or tuktuk or coach, the latter two to be preferred if traveling with kids, all of them pretty cheap to a western audience.

A 1 or 2 USD ticket (still cheap) is required at the entrance of the protected zone and then, once you get to the dock, you can negotiate a longer or shorter tour of the village and the surrounding area and lake.

The characteristic boats, featuring the propeller attached to a long and slender shaft and powered with second hand diesel car engines are often driven by young sailors in their twenties or thirties, and several of them have their families and kids aboard, when the boat is not too crowded. In my tour, aboard the boat there was just me, the driver, his young wife and their two nicest kids, 5-6 years old the elder, only a few months old the younger. Waters are calm and the atmosphere is suitable for all ages!

Finally, I visited in December but I could claim that February is still an appropriate time for visiting. This is one attraction that one can plan the day before, to leave after lunch and come back to Siem Reap for dinner time. I have honestly no idea if it makes sense or not to visit Kampong Phluk on your way from Siem Reap to another city, either by coach or boat.

Here is a 9 minute video from some clips I shot when I visited, on Dec. 3, 2018; here instead crocodiles in a breeding farm at the edge of the town on the same day.