By "cruising the Rio Dulce" do you just mean the Rio itself? For the entire time (April - Nov)?
Spending the entire rainy season on the boat could get a bit claustrophobic so I suggest: use the boat as early as possible on those date like April - May and then travel inland to avoid most of the rainy season. There are periodic security
problems on the Rio so I suggest sticking to marinas
or at least more popular anchorages
Ive had cruising friends who've spent time on the Rio and around Guatemala with young kids. On the Rio they prefered the marinas Tortugal and Nanajuana. Both of which have room to roam for the kids. I think that Tijax or Catamarans would probably be good too.
They also rented a house on Lake Atitlan and lived there for several months....beautiful area.
Guatemala is an amazing country with plenty to see and do. Security
is usually not a big concern, but use common sense. Guate does indeed have big problems, but most crime involves drug trafficking and gangs. The typical visitors are not affected, but bad things to happen sometimes. The probabilities are low though, of the millions who visit Guatemala only a few have issues with serious crime.