macOS Sierra doesn’t seem to remember SSH keys between reboots
As of macOS Sierra 10.12.2 Apple added an ssh_config option called UseKeychain which allows a 'proper' resolution to the problem. Add the following to your ~/.ssh/config file:
Host *
   AddKeysToAgent yes
   UseKeychain yes     

From the ssh_config man page on 10.12.2:

UseKeychain
On macOS, specifies whether the system should search for passphrases in the user's keychain when attempting to use a particular key. When the passphrase is provided by the user, this option also specifies whether the passphrase should be stored into the keychain once it has been verified to be correct.  The argument must be 'yes' or 'no'.  The default is 'no'.