I've been to many of the New England Zoos and Aquariums, And I would probably say Roger Williams is the best in New England. It may not be huge but when compared to everything else nearby it is certainly better looking and has a solid lineup of species. I went back in 2012 when the old rain forest building was around and it was still very nice. I really want to go back someday to see the new one when it is done. As for my rankings of zoos and aqauriums I have been too this is the order I would put them in.
1. Roger Williams
2. Mystic Aquarium
3. Stone Zoo
4. NEA
5. FPZ
6. Beardsley Zoo
7. Maritime Aquarum
8. Maine Wildlife Park (Not technically a zoo, but has many native species)
9. Maine State Aquarium
10. York's Wild Kingdom
I actually prefer Stone over FPZ, I like the rain forest at FPZ but after that Stone zoo is a nicer overall experience. And I don't mean just animals but the way the zoo looks and is laid out and amenities. Im also not a huge fan of the New England Aquarium, but it does have a great collection when compared to Maritime. The Maine Wildlife Park is also on this list because while it technically isn't a zoo, it does have exhibits featuring Maine Wildlife, most which has been rehabilitated and/or cannot be released to the wild. they have a great Moose exhibit and has renovated their Black Bear exhibit.
It is strange though when you think about New England zoos, because look at zoos in their western neighbor, New York and for the most part they are vastly superior. Seneca Park, Buffalo, and Rosamond Gifford in upstate NY all appear to be superior or equal to Roger Williams. Personally Rosamond Gifford is my favorite of those zoos, and is a great model for colder-climate zoos. Also obviously the down-state zoos in NY are of pretty high quality, with the Bronx Zoo drawing a lot of visitors from southwestern portions of New England.
The NE Aquarium is not bad, but boring in my opinion. Its got a nice collection, but the concrete look and exhibit layout are pretty meh. Its similar to the National Aquariums original building, yet that aquarium has greatly renovated that space, with better displays, species and flow. It has the best fish collection in New England, but since Mystic is more mammal heavy that makes sense.