You can run Migration Assistant multiple times. Probably the simplest method is to make a TimeMachine (or "clone" such as with Carbon Copy Cloner, SuperDuper, TechTool Pro, etc.) backup of the "old" computer and then run Migration Assistant on the new computer and connect the backup from the old computer and instruct it to migrate over the user account (and only the user account) from that backup. You can run Migration Assistant multiple times if the backups are separately made on different Macs.
This process works smoothest if you don't have any user accounts on the new Mac with the SAME USERNAME as the one being migrated from the old Mac. (It is still possible to do this but it is simplest if you avoid that situation.)
In your situation, follow Leroy's instructions on using Setup Assistant on the very first boot up, migrate over one of your user accounts, and then you can run Migration Assistant an additional time to migrate over the second user from his/her backup separately.