We booked Oriental Sails which does not charge children 5 years and below.
Also, they offered a small bed for my girl (free of charge) so we all slept comfortably together in one room.
I must say that El Nido, Palawan in Philippines is much better because I am biased. Haha.
El Nido offers island hopping tours A, B, C and maybe D as well so we were able to visit several of these small islands and most of them have nice beaches.
With Halong Bay, we were able to check out one island only. But maybe because we only booked for an overnight trip so we are limited on time.