I live in Brooklyn and still get plastic bags at three different grocery stores I can think of. (I reuse them as trash can liners, so the ban always seemed silly to me — I’d need to start buying my own plastic bags in addition to the paper ones I recycle.) There was a week or two that most stores switched to paper, so you may be seeing paper-only bags from stores that have unused stock to go through. Some grocers (Whole Foods) have always been paper-only.
New Hampshire, Illinois, and Massachusetts have specifically banned the use of reusable shopping bags in grocery stores state-wide on sanitation grounds. San Francisco has as well. I was confusing these with NYC when I commented above. NYC’s enforcement delays are unrelated to concerns over reusables.