I have a file that our customer encrypted using our public key. I know how to decrypt it using our ppk file programmatically, but I am unsure of how to do this from the command line, or using PuTTYGen (which I don't think supports the decryption of files from the utility).
Why do you have a public key if you don't know how to use it?
The encrypted block probably says in clear text what program/system was used to encrypt it. It's probably the one that generated your public key.
BTW, I believe I've seem phishing email that used this scheme to try to trick you into downloading and running some "decrypting" software.