For simplicity for visitors arriving for a few days, I recommend getting seven-day LinkPasses for the T- it’s $19 for unlimited travel on subway and local bus services, and makes it much easier to go through the turnstiles than buying a ticket each time you go. Info on passes is here: http://mbta.com/fares_and_passes/passes/. You can buy passes from the machines at any T station. If you really need a cab, I strongly recommend Boston Metro Cab (and they didn’t even pay me anything)- http://boston-cab.com/

Boston Harbor Cruises and the whale watches go from Long Wharf: http://www.bostonharborcruises.com/ (historic sightseeing cruises are here: http://www.bostonharborcruises.com/boston-harbor-cruises/historic-boston-tour/schedule-rates/)

Everyone forgets about the Harbor Islands, which are a wonderful day out and have something for everyone, from historic forts to good hiking trails and activities for all ages. Info on the Boston Harbor Islands National Park area (and ferries out to the islands) is here: http://bostonharborislands.org/