If we're talking moral equivalence then I'd say the person actually in an official position is worse than the regular old citizen without any official power.
Actually that's precisely why Kerry's is worse. The purpose of the Logan Act is to prevent unauthorized people with no authority from negotiating on behalf of the United States and undermining its foreign policy. Flynn was just a few weeks from being authorized, and such authorization was certain. He just spoke too soon. Kerry is actively trying to get a foreign power to blow off the Administration that's going to be in power for at least the next 2 years and maybe longer. At least in terms of violating the intent of the Logan Act, Kerry's acts are worse.
As a practical matter, will either be prosecuted? No chance in hell. The Logan Act is a joke - hasn't been enforced in literally centuries.