1 the person who leads or commands a group, organization, or country: the leader of a protest group.
• (also Leader of the House) (in the UK) a member of the government officially responsible for initiating business in the House of Commons or House of Lords.
You're arguing the second definition, which is specific to the UK.
Anyone can lead a protest, especially small ones. To be "the leader of THE opposition" you need supporters in great numbers in any country. Navalny simply doesn't. The polls show quite clearly that other politicians who run against Putin have higher name recognition and more popularity.
Just look at yourself - if hard polling data that contradicts a specific statement of fact can't convince you, nothing ever will. You'll always find yourself falling back on trying to argue that technically the NYT's statement doesn't mean what it seems to mean regardless of what counter-example is picked.
Regardless of what you may personally believe about Russia or its politics, the statement that Navalny is "leader of the opposition" is simply 100% factually false by any hard, observable data.