Are you going soon? Please make sure that you don't go on Sept. 1. If I remember correctly, Sept. 1 is move in day for many college/universities in Boston or surrounding area. It is so congested everywhere and it is difficult to find a parking.
Last week of August through the first week of September is moving hell in Boston/Cambridge.
I hadn't heard of the Boston Card but it seems to be a decent value provided that you can organize your trip to take advantage of multiple sights. The Boston edition of the Entertainment Book has many B1G1F admission coupons to all but the most coveted attractions, even so, the Boston Card may be worth it.
Definitely skip the Franklin Park Zoo.
Look into going to Georges Island in the harbor, Fort Warren [haunted Civil War fort & prison] is out there.
http://www.bostonharborislands.com/georges
The Freedom Trail is free and has free guided tours led by park rangers.
http://www.nps.gov/bost/planyourvisit/guidedtours.htm
Fenway Park is a must see for any baseball fan.
If you delay the trip until April, you can catch the re-enactments of the battle of Lexington & Concord.
Walk through Harvard Yard & around Harvard Square. Don't forget to get an ice cream cone from any of the terrific ice cream shops between Harvard & MIT.
If you want historic, there's the Union Oyster House, the oldest restaurant in the US.
http://www.unionoysterhouse.com/ They are not cheap.
Unless you both hate seafood, there are tons of wonderful restaurants right on the harbor that have unbelievably fresh fish.
If you love plants, the Arnold Arboretum is a must see.
http://www.arboretum.harvard.edu/
There are selected hours during the week when most of the museums are free or reduced admission; but that is difficult to squeeze in during a short trip.
Do not rent a car or attempt to drive. The T is fine & will get you around town when you don't want to walk.
Best piece of advice is wear comfortable walking shoes.