I suggest you first offline any resource groups you may have configured. After that you can just reboot the servers at will, it is just important that if both are down, start them up one at a time. Autostart does not like when multiple agent services start at the same time. Apart from that, there are no special considerations.

Should I shutdown the nodes and take my SQL server instance offline before I reboot? I don't have any resource groups configured.

Actually MSSQL instance is also a resource group, but you don't see it unless you use "advanced" option in the Autostart console, so the answer is yes.