Since squash, corn, and beans are the famous "three sisters" of American Indian agriculture, how come we don't have beans as a staple at the Thanksgiving meal? Were beans grown in Massachusetts at the time of the first Thanksgiving and were they served back then?

Green beans are indeed beans! Just young ones. (Pretty much anything called "bean" in English is indigenous to the Americas, except for fava/broad beans and soy beans.) Of course they wouldn't have been eating green bean casserole in colonial times, though; it was a mid-20th century invention, which should come as no surprise considering all its requisite ingredients come from cans.