Visiting Boston is about the the atmosphere, history, the contrast among the different areas and buildings.
That's why Freedom Trail is the best choice. It’s a rute made by the city hall that drives you through the city. You can do it by yourself (following the red line on the street) or you can enroll a guided group.
Wake up early and you'll be done after lunch time so you have time to visit Bacon Hill, the University Area, Fenway Park or the Red Sox Stadium.