If you are happy with Citadines then go with that. My data points for serviced apartments are slightly older, but typically I would have stayed at Citadines (or its related properties). Incidentally, the BTS should be fine to travel on even with small kids - it's generally faster than taking car and it's air conditioned. The only times I would avoid it, is during the morning and afternoon rush hours and if it is raining like crazy. These both tend to be times when the train is jammed. Also, I have found Thais to be generally respectful of personal space on BTS, so from my experience at least, it's a pleasant experience.

In any case I hope you have a great time in both Thai locations. Please do share some photos/reviews.