There is NitroKey[0], which seemed to me like a good alternative to Yubikey, but I haven't ordered either yet so I can't say I have first-hand experience. But much luck if you decide to go with it, something I'm looking more and more into, especially since I too use password-store and it would be good having an easier to use setup that is still secure.
Nitrokey claims on their homepage that the firmware of the Storage version of NitroKey can be updated by software. This seems to mean that there's someone out there with a key that can sign arbitrary code that can be loaded as an update and gains access to the crypto material on the device.
I had a look through their instructions and I'm not sure if there is a signing process that happens. You have to enable firmware access from the app, and then it's a bog standard DFU flash to load the new firmware.
But there were some important differences. Newer GnuPG versions have simplified how gpg-agent takes the place of ssh-agent. Nowadays, it's enough to create an SSH_AUTH_SOCK environment variable that points to ~/.gnupg/S.gpg-agent.ssh
Also, I found the air-gapped system setup described there and elsewhere to be excessively difficult. Far and away the easiest way to create an air-gapped key generating machine was to install OpenBSD to a USB key (you can boot the mini install image and overwrite the same device). Installing the gpg2 package gives you a complete gnupg environment for interacting with OpenPGP smart cards. By contrast, there were a bunch of packages to install with Ubuntu / Debian.
It was a little hairy to set up in total, but I really love my Yubikey-mediated GPG setup. I also now use password-store for passwords, complete with dmenu integration.
I'm not super happy that the Yubikey 4 isn't 100% open hardware though. If someone has a recommendation for something that is, and supports 4096 bit keys, I'd gladly hear it.