There are lots of great things to do in Boston. You should take a walk through the Public Gardens. The swan boats aren't running yet, but things are starting to bloom and it is pretty. Once you walk through the Public Gardens, you can stroll up Newbury Street if you and your sister like high-end shopping. Personally, I never go there, but I know a lot of people at least like to window shop.
The day you go to the Aquarium, there is a Legal Seafoods restaurant nearby...a Boston classic. You could also walk to Fanueil Hall from the Aquarium and do some shopping or walk over to the North End. There are so many great Italian restaurants there...Pomodoro is a favorite with my family. While there, you should pick up some cannoli...my favorite is at Modern Pastry, but Mike's is the bigger name. They are both on Hanover Street. While in the North End, you can also visit the Olde North Church.
If you are into sports, take the green line to Kenmore Square and take a tour of Fenway Park. After you're done, you can have lunch at Boston Beer Works. They have great burgers and beer...my favorites are the Boston Red burger and the Fenway Pale Ale.
If you are more into the eclectic, take the red line to Harvard Square and walk around. It is a very interesting place with lots of quirky, fun shops. If your husband is able to join you for dinner, you could try East Coast Grill in Inman Square in Cambridge. You would be best off taking a cab, as it is a little ways from any T-stop. It would be a short ride from Harvard Square. The food there is delicious. It's owned by Chris Schlessinger.
If you can't go to dinner, you and your sister could go to Jaspar White's Summer Shack. It is a short ride on the red line from Harvard Square. Just go to the last stop, Alewife, and you'll see signs for the restaurant when you get outside. The place is very casual, but the seafood is terrific. The fried clams are the best I've ever had and the raw bar is fantastic, if you're into that sort of thing. They have daily specials too, and of course, great lobster. Try the pan-seared lobster if you're feeling decadent.
Well, that list should get you started anyway...have fun!!