macOS Sierra doesn’t seem to remember SSH keys between reboots I have to run this command since upgrading to macOS:

ssh-add -K


Corrects the problem after the reboot but I have to run this command every time I log on to my computer.

If I do not run the command above, my keys in ~/.ssh are skipped and I am being asked server password in order to establish the connection.
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'.