I believe there are many suggestions in the site already, but I wanted to share the answer, in case someone else need the information:
Having two boy 6 and 9 myself, here is what I recommend:
Guatemala Zoo, a full day activity, you can spend all day there, half on the zoo, and half of the mechanical games. Closed on mondays
Children´s Museum, in front of the zoo, for a full afternoon, It closes on midday, but get to there early, as time will not be enough, maybe from 2:30 thru 5 or 6
Relief Map, or Mapa on Relieve. It is a great place to see the whole country, in miniature, also there are mechanical games there.
Laser Hero, at Centro Comercial Pradera or Pradera Concepción. Gotcha but with laser guns instead of paint balls
Parque Cayalá (not to be confused with Paseo Cayalá) for a walk in a forest without leaving the City. There are two parks there, very similar. Paseo Cayalá is nice also, but there is not much to do there with children, except have lunch.
You should really try to go Irtra in Reu (Retalhuleu) is a two hour trip, and spend there at least three days, including a weekend when the parks are open, monday everthing is closed, except some pools. It is a must for your children, no matter what.
Irtra Petapa, is a small version of the site at Reu, but a great place to spend a day, also closed on mondays,
Movie theathers at Okland Mall or Miraflores are great, but children movies are in Spanish, most of the time. At Miraflores you can also visit the museum.
Parque La Democracia is a very nice park, to ride bikes just around
Bowling at Metro Ball Zona 15 or Tikal Futura in zona 11.
Ruins at Kaminal Juyu in Zona 7
If you are going to Antigua, visit the ruins, specially Capuchinas, Santa Clara and Catheral. Also if you can stay a night a Casa Santo Domingo it would be great. Also Finca Filadelfia is a great visit.
Iximche ruins and Tecpan, are about and hour and a half a great place to be.
Mixco Viejo ruins is another great Mayan site about an hour from the city, but take your lunch with you, and make a Picnic, there is nothing more than tortillas there.
Amatitlán Lake is about 45 minutes from Guatemala City, you can go to the town of Amatitilan to see the lake, take a ride on a boat. You can algo go to Parque Naciones Unidas, I haven´t been there for a while, but it has reproductions of some places in the country, and was nice. Or you can go fishhing in El Relleno, if you don´t mind being followed
by 20 more children.
On Sunday morning you can go to Pasos y Pedales in Avenida Las Americas.
Cerrito del Carmén, has been refubrished and last time I was there it was very nice.
Cervecería Musuem at zona 2, I believe you have to make an appointment
Museo del Ferrocarril at zona 1.
I enjoyed a visit to El Amate, where you can buy fake brand name everything and pirated movies with a secure parking.
I haven´t been there in a while, but walking on 6a Avenida is supposed to be very nice, including a visit to Central Park, the Cathedral and maybe the National Palace
Depending on thte date, you can look for a Fair, they are very nice.
Hope this helps, I guess you can have a great time here.
Hope this helps somebody else too.