Boston is familiar to us as our daughter lived here for 5 years and we know the lay of the land.
The sells a shuttle pass from the dock to Quincy Market which is right downtown for $16 per person but you can take a cab for around $12 plus tip.
Skip the excursions as you can do everything that you want on foot and see way more.
Send away for a Boston Visitor's guide which will provide you with everything that you will need for a great visit.
Don't forget to visit the Italian North End for some fabulous pizza at the Express pizzeria on Hanover Street as well as pastries and cookies at Mikes Pastry or the Modern Bakery on Hanover as well.
Boston Commons, Public Gardens and Beacon Hill are all worth the visit.
On Cambridge and Charles is an old jail that has been converted to a classy hotel with a great restaurant called "Scampi" which is a little pricey but fabulous.
There are two "Cheers" restaurants around for the tourists that cannot resist the traps