Hi,
I have just read you question.
First of all you must know that Yad Vashem is overwhelming. I don't think young children will be able to acquire and understand the topics presented. Even in Israel itself there is a debate regarding how to talk with young children about the holocaust. This place is not a Jewish museum that you can find in several European cities, like Berlin. It is different. I would say it is even more than the Japanese peace memorial park in Hiroshima. But, I don't think you will be able to understand it before you have been there.
Secondly, the science museum nor the zoo are much close to the Yad Vashem site. This means that for the science museum it will take you by car about 15 - 20 minutes and to the zoo, more. I would recommend that if you are to choose one museum, go to the Israeli museum which is in the area of the science museum. There, you could spend around half a day or more between the exhibitions. Near it is the biblical land museum, which is smaller, but I think is more unique than the science museum (which is nice, but rather small for what you can find in Haifa or abroad). I think your children will have more fun in these museums. As for the zoo, it is superb, you can spend there half a day or more if you wish and it is good for all ages, from toddlers to elderly persons. In my view, this zoo, is standing along other great zoos in the world. But again, it is much farer than Yad Vashem.
And last, near Yad Vashem there is the area of Ein Karem. You will need a car (or wait to the bus). There you can visit some churches, if it is in your mind, or go to one of its restaurants. I don't say children will have much to do there, but maybe for an hour or so, you will find there what to do and it is about five minutes car ride from Yad Vashem. Another Thought, Yad Vashem is not very far from the last stop of the light train. Maybe you could be with your kids in the city center and then take the train to Har Herzel, which is its last stop. The ride itself is very easy and nice and you see several sites of Jerusalem. The only thing is that you have to buy tickets from the automatic machine in the train stop, before you go to the train and once onboard you have to validate them.
Regards...