As a non-New Yorker, I would not know how to pull a list of "all NYC real estate that has a judgement lien," but if there are particular parcels of real property you are interested in buying, another inquiry would be whether there is a lis pendens filed on those parcels in the counties where they are located. The lis pendens is a public record--a notice to potential buyers that there is a cloud or pending litigation that might affect the buyer's ability to gain clear title. Not sure if that covers all that your question contemplates, but this would be one more tool in your toolbox.
The last time I used the ACRIS system was a number of years ago. At that time there was no way to run the report you seek. Consider condulting with and possibly hiring a title company to get the information if it is even possible to do so.