I have to disagree with some of the above. I also live outside of Boston but work in Boston daily.
I would not visit Ruth Chris or Abe and Louie's with a 7 year old, we did Ruth Chris last year in Boston and it was Awful and not work the money we paid.
Fenway park - laughable - you'd need a second mortgage for tickets to those games and you even might need to sell your 7 year old
You can definitely get arund on the T and they do a a daily pass and a weekly pass. Using the Charlie card (a refillable card is $1.70 each way and using a paper card is $2. See link below.
http://www.mbta.com/fares_and_passes/subway/
I'm not a fan at all of our aquarium, but money better spent might be a whale watch, you can also combine that with an aquarium ticket. The whale watch can be ALOT of fun.
Big fan of the science museum, there's also the Children's museum which if you happen to be in town on a Friday night you can go for $2 a person after 5:00 which is plenty of time.
I'm not sure when the swan boats get put in, but thats also fun and very reasonable. You can also see the duck statues in the Boston Garden. Fanuiel is also very fun and there's also street performers there, especially on weekends. Depending on when you will be here in April there's the Boston Marathon on April 16, but that also makes it a very busy time in the area and hotel rooms will be at a premium.
I'd also plan on doing dinner in the North End - my personal favorite is Giacomo's. Mike's pasty is excellent, but if you are a true north ender, then modern is what is recommended, but I prefer Mike's. Alot of resturants in the North End are cash only, so just something to consider.
You best best for hotel rooms may be on the outskirts and then taking the train in daily. There's the Quincy Marriott, which is very nice. Braintree has a super 8 motel - but I would not recommend that.
If you have specific recommendations, but let me know and I'll answer anything I can.