Here is the solution from the link I posted in my comment. This comes from here, which references this superuser post.
.ssh folder in
/home for the keys to be stored
sudo mkdir /home/.ssh
Move existing authorized_keys file into
.ssh dir as username
sudo mv ~/.ssh/authorized_keys /home/.ssh/username
Create symbolic link to authorized_keys file in user
ln -s /home/.ssh/username ~/.ssh/authorized_keys
sshd_config file to set the new path for the
sudo vim /etc/ssh/sshd_config
AuthorizedKeysFile line to:
Reboot the computer
sudo shutdown -r now
Login to your server and you should be presented with a minimal un-decrypted home directory... You will need to create and edit a .profile file in there to get
ecryptfs to mount your home directory.
sudo vim ~/.profile
Add these lines:
Log out/Restart, and go back in again. You should be prompted for your password after SSH key auth, and then be presented with your decrypted home directory.
You should now be able to login using SSH keys every time, no matter if your home dir is decrypted or not.