Having grown up, 20+ years, with Stone zoo being my home zoo, I agree with your opinions. Stone is a small but excellent zoo. Can't wait to see the new Caribbean addition. However, Southwicks is head and shoulders above both Roger Williams and any other New England zoo that exists. Like Stone, it has grown and developed immensely over the last two decades. The enclosures and collection (anybody like Vicuana?) have far surpassed any other zoological facility in the area, AZA or not. FPZ is still a disappointing major city zoo, especially for Boston. Buttonwood, Stone, Capron and Beardsley are great but don't have the size, collection or exhibits that can compete. And, from my point of view, RWP's one species I like seeing, will be phase out in the long run, African Elephants. Almost all other species there can be seen at other zoos in New England that have more eye pleasing enclosures. For my money, I'd go to Southwick before visiting any other facility within the six states.
Also, not too long ago, York made a run at being one of the best but money and ownership never saw this come to fruition.