Finally got out to a couple of the harbor islands: Spectacle island and George's island. This is a good outing, especially if you have a mixed age crowd. In this case the youngest was 5 and the oldest was 80. A good time was had by all, but make sure you bring sunscreen and a water bottle. It can get pretty warm in the sun.
Boston harbor is really an archipelago, even if it's not usually referred to that way. Definitely worth heading out into it at least once just to see things from that perspective. Short of having your own boat and cruising around, this is a really good way to go. I'm not into camping, but that's also a possibility.
Have a look at the boat schedule to plan a bit. Touring around for 4 hours seemed like a pretty good excursion length, and you can comfortably do a couple of islands in that timeframe. Fort Warren is kind of neat to walk around in, then pick one other where you can at least put your feet in the water.