Yup Ned's is still around, I've only been there once but I loved it. Not only did they have a great selection but the customer service was amazing, the employees will happily take time to give you a guided tour around the store provided they aren't too busy.
Tropical Isle in Framingham is really cool too, I have never been to a store with so many tanks.
Pets Plus in Tewksbury is pretty good but it's kinda small.
Aquaworld in Chinatown might be worth a trip, especially if you can have a look in the back room.
Lovely Pets in Quincy is good too.
These next ones are not exactly in the Boston area but are worth checking out if you ever get the chance.
Pet City in Seabrook, NH usually has a decent selection.
Zoo Creatures in Plaistow, NH is expensive but worth it to see the displays especially if your a reptile guy.
Lebanon Pet Center in Lebanon, NH is pretty far from you but worth stopping buy if you are ever in the area.