Ahhh.. Thank you for the itinerary...
I suggest you pack slacks, jeans and light sweaters... a few shorts just in case it gets hot. I also suggest a light jacket depending if any of your excursions are on the water.
Yes.. layers is the key. Boston is wonderful place with so much history. I hope you have time to look around. If you do and want to live a little history.. go here... http://www.celticweb.com/greendragon/
I know you'll enjoy your cruise no matter where you go.