I might recommend different Northeast zoos based on things like where you are close to, and what qualities you look for in zoos (do you have affinity for particular types of animals, or do you prefer particular types of exhibits?).
Regardless, out of the options you have listed, most people would probably recommend the Bronx Zoo as the top Northeastern zoo to prioritize, as it is consistently ranked as one of the best zoos in all of North America. The zoo is huge, has amazing exhibit quality, and lots of rare species. The Bronx Zoo is also a very historic place, and they spend more money on conservation than any other zoo in North America. It will take at least one full day (possible 1.5-2 days) to see everything there.
After the Bronx Zoo, I would probably recommend the Philadelphia Zoo in second place. This zoo is known as the originator of "Zoo 360"-- a form of zoo design where animals have access to a network of enclosed trails that allows them to roam all around the grounds, far outside the constraints of their normal exhibits. The Philadelphia Zoo is also known for having a lot of rare species, but there are fewer rare animals there nowadays than there used to be. The Philadelphia Zoo is not known for their exhibit size or quality (outside the Zoo 360 trails), and overall the place is much smaller than The Bronx Zoo.
The Roger Williams Park Zoo is nice too (especially if you live closer to Rhode Island than to New York or PA), but I personally prefer Bronx and Philadelphia more. Some other good zoos in the northeast that you didn't mention, but which may be worth considering, are the New York Aquarium, Central Park Zoo, Mystic Aquarium, and Rosamond Gifford Zoo.
