My 3 year old son have a high fever for three days and just started vomiting today. His sister has a fever also. What could this be? What should I do

Probably viral but.. It is impossible to know for certain from these symptoms, but the most likely cause is a viral infection, possibly roseola, which is common in 3 yo's & has high fever with few other symptoms (though vomiting can be one of them). Classically the fever goes away after 3-5 days & then a rash appears, so it may be hard to know if he has this for a couple more days. Please see "comment" below for more.
Some tips. 3 days of fever and vomiting - take your son to see a medical provider - urgent care or er these days. It may be a simple cold or the flu (more likely) or may be a stomach flu (viral gastroenteritis). Vomiting can lead to quick dehydration, so you should seek help promptly.