I don't know if I would call any of those 'in the area' for Boston.
Unique Aquaria moved to Tewksbury
I believe Krystal Klear is closed. Couldn't find it and the number no longer works
The Fish Nook and Unique are resonably close. You could pull off Unique, The Fish Nook, Uncle Neds, and Tropical Isle in one big loop if you wanted to and didn't have much to do for the day.
I think you are going to need a vehicle to get to any of them from Boston though. I don't know if Unique is accessible off the commuter rail.
I usually feel kind of guilty using the quick reply... my replies are rarely quick.