If the wiring between the units is completely separate, then yes, separate boxes. If the wiring is mixed, you'd have to fix that before you can do separate boxes and meters. Same with water, gas, etc. Depending on what systems looks like will determine if separate is even possible.
My parents own a duplex. There are 2 electric meters, the wiring and boxes are separate. There are 2 gas meters but one gas line in. But there's only 1 water meter. Each unit has their own gas and electric accounts, and the owners (my parents) pay the water bill and have increased the rent amount a tad to reflect it.