Another vote for the shuttle to the Blue Line instead of the Silver Line. Just the other day, I took the Silver Line from the airport, and it took close to 45 minutes to get to South Station from when I started waiting.

The Freedom Trail is great, but as has been said, it is a lot of walking. Some alternative ideas are to take a walk along the harbor. This is one of my favorite areas of the city. It has great views of the city and the various landmarks on the water, like the courthouse or the World Trade Center.

They could also take the Red Line to Harvard Sq, which IMO, is a pretty neat area. From shopping to eating to viewing the campus, it's all pretty fun.

Another thing I tell people to do is take the E Green train to Prudential and check out the observatory on the 50th floor of the Prudential Center (or 'The Pru'). It costs $12, but the views cannot be beat, and you could spend a long time up there checking out the great history of the city (they give you devices). On the ground level, there is a lot of (indoor -- mall type) shopping here.

The ship yard in Charlestown is also neat. It houses USS Constitution and another ship. Tours are available I believe.

If tours are what they want, the Boston Duck Tour is something that I've only done once (and a long time ago), but I do remember that it was fun, and educational. They use authentic WWII amphibian vehicles that give a tour of the city on wheels, and the they take a dip into the Charles River.

There is a lot to do in the city. Out of all of them though, one of my favorites is simply walking around, without a certain destination in mind. They don't call it The Walking City for nothing!