The court ruled that the charities had funded the militant group's activities and so were liable to pay compensation to the family, which had sued under a federal anti-terror law.
Three organisations - the Quranic Literacy Institute, the Islamic Association for Palestine and the Holy Land Foundation for Relief and Development and an alleged Hamas fundraiser, Mohammed Salah, were also held responsible.
Earlier, a federal jury ruled that Stanley and Joyce Boim were entitled to $52m compensation, but Judge Arlander Keys tripled that award.
The assets of the three outfits and Salah were frozen following the ruling.
However, reports said it was unclear how much the Boims would actually receive, since the charities already have other cases pending against them.