Its education committee investigated after 12-year-old Stuart Cunningham-Jones died in a bus crash in Ystradowen, in the Vale of Glamorgan, in December 2002. An inquest found the driver could have been distracted by pupils misbehaving.
The Assembly report recommends all children on a contract school bus should have a seat belt, and that the "three-for-two" system - where three children can sit on seats designed for two - should end.
It also calls for double-decker buses to be phased out from school runs.
Most recommendations are up to local authorities to carry out, but altering the "three-for-two" system would require Westminster to act.
Pat Harris, from safety campaign Busk, said the recommendations were "good, really good, but only if they are implemented".
David Cunningham-Jones, Stuart's father, said the recommendations would answer the questions about what price is put on a child's safety if implemented. "On behalf of the children, we thank you," he said.
Peter Black, chair of the Assembly education committee, said: "Safety is of paramount importance." He said there should be incentives for operators to invest in better buses and staff training, adding: "I believe there is a genuine will to make school transport safer and more enjoyable."