Taken from this ServerFault post: https://serverfault.com/questions/603982/why-does-my-openssh-key-fingerprint-not-match-the-aws-ec2-console-keypair-finger
Keys generated locally You can use OpenSSL, as demonstrated by Daniel on the AWS forums, to generate the fingerprint in the form used by AWS to show fingerprints for uploaded public keys (SSH2 MD5), like:
7a:58:3a:a3:df:ba:a3:09:be:b5:b4:0b:f5:5b:09:a0
They can be generated by extracting the public part from the private key and hashing it using: