Solution 1 (recommended)

Apple updated its Technical Notes to indicate that since 10.12.2, macOS includes version 7.3p1 of OpenSSH and its new behaviors.

In ~/.ssh create config file with the following content:

Host * (asterisk for all hosts or add specific host)
AddKeysToAgent yes
UseKeychain yes
IdentityFile <key> (e.g. ~/.ssh/userKey)