No it's not. First the very first sentence: Any citizen of the United States, wherever he may be, who, without authority of the United States: Clearly putting it up to a vote would be authorizing, giving authority to Congress. It's not like Congress is going rogue to meet him privately. It would be authorized by vote and public.
Then: with intent to influence the measures or conduct of any foreign government or of any officer or agent thereof: If Netanyahu is speaking to Congress, there is no evidence congress is trying to influence him, so that doesn't fall under it either.
Though the second part doesn't matter so much, since the first part allows for authorized discussions under the law. It's unauthorized meetings with foreign nations that were clearly the intent of the Logan Act to prohibit.
That is not even close to Congress voting to authorize a speech on the floor to a member of another nation to speak to them.