Base64 changes representation so bytes survive text transport. Encryption changes representation so only the holder of a key can read the data. Only one of them provides confidentiality.
01Choose by purpose
Need data to survive a text-only channel: Base64.
Need to keep data secret: encryption.
Need to detect tampering: a message authentication code, not Base64.
A practical guide to choosing random passwords and tokens, deriving and storing password hashes, signing tokens, encrypting with authenticated modes and measuring entropy.