I did the duck tour in Boston, it was great fun! I loved how the vehicle was land and water! If you like Italian, there is a fab restaurant, which only the locals really know about (well I guess not anymore! called Pasta Presto. It is just north of 42nd street (Grand Central Station) by about 6 blocks on the left side of the road. So it is basically at 48th and 7th. In saying this, I've not been there myself since 2002, but I know of others who have been within the past two years and still rave about it!
As for the sites, Ground Zero is worth a visit, it is a very poignant site, and although I have personally not been there since the monument was erected, others have said it is still as poignant as it was. Battery park is beautiful to sit and have a picnic in. Central park, go to the zoo, it is great fun! You have not said when you are going, but if it is post May and into the summer, they have open air theatre and bands that play, very often for free. The broadway and off broadway shows are fantastic...and the shopping from about 52-58th is superb! Also, Chinatown, and Greenwich Village are great even for just a stroll. (I have been to NYC many many times, and just speaking of what I used to love to do!) If you are into celebrity spotting, the village is always almost a guarantee, as well as the upper east side!
For Boston, I mainly hit the shops as well, is it just Boston, or are you getting to Cape Cod/Marthas vineyard as well? They are beautiful places to visit if you can get there, if you are, the whale watching tours are great! Have only been on two weekend trips to Boston, and one was mainly shopping, the other was seeing the major sites. We did a city bus tour, one of the hop on and off ones, as found that to be the best way to get around.
Hope you have a great time! Will be interested to hear if you are into Italian, and do check that restaurant out!