None of the roommate drama adds up to a legal point worth debate.....what matters if your lease and your local laws as to renewal options.
As a practical matter your roommate is free to have a live in friend that you don't like and he need not like your choice of live in friend. Whether the live in friends morph into tenants with rights requires more homework as to your local NY rules....often a live in roommate does acquire tenant rights in NY.
This may be a case of the Ll really doesn't care who lives there just so he gets paid...and you either crank up the bully power or make plans to move.

