What is the best way to shut down a 2 node availability group
No need to touch the AGs.  You should have full set of database backups on a USB external drive or on Azure Blob Storage before you shut down the datacenter.
Just shut down the secondary node first, then the primary.  Bring them back up in the reverse order.  Boot up your domain controller VMs first, then any other supporting infrastructure, like the VM hosting the FSW.  When you bring the VM hosting the primary replica online it should establish quorum and come online.