There is a relevant Q&A here about how ex post facto is defined in the United States.
Not all law is about crime, and that includes NY rent control laws; violating them does not lead directly to a criminal prosecution, hence a sufficiently strict definition of ex post facto cannot apply to them. And such a sufficiently strict definition has been the explicit one since 1798, when the Supreme Court ruled in Calder vs. Bull ("law that makes an action done before the passing of the law, and which was innocent when done, criminal [...] law that aggravates a crime, makes it greater than it was [...] law that changes the punishment, and inflicts a greater punishment, than the law annexed to the crime", etc.).
Notice that Article 1 Section 9 prohibits Congress (i.e., the Federal Government) from doing exactly the same thing, so if ex post facto refers to any kind of law, then there could not be any retroactive laws passed in the United States, period. However, the Supreme Court has apparently already set further, more recent, precedents, making it clear that this rule does not apply to tax law.
I would assume in this case the intention is to retroactively extend the old law, i.e., if the old law expired on the 15th and the extension passes on the 20th, that extension will be retroactive to the 15th. If the extension then continues until a new law is in place, there will be no time period under which one or the other did not apply. Despite the wording in the news article, I do not think the intention is to make the new law retroactive, only the extension of the old one, for the simple reason that the legislature would never agree to pass such a brand new law later and no matter what it contains say it will be retroactive back to the original expiration date of a law it replaces even after they already extended that until there was a new law. That is borderline non-sensical. The Daily News blurb certainly makes it sound like it might be that way, but I think this is a bit of intentional obfuscation -- the way in which a partial quote is used in the first paragraph is indicative, and the Daily News is, well, the Daily News.