The seal shows an Indian armed with bow and arrow and wearing a loin cloth who speaks the words "Come over and help us". It refers to a Biblical vision of the Apostle Paul which was used to justify the missionary journey to Europe (Acts 16:9 "Come over into Macedonia, and help us."), applied here to Europe's relationship to America.
Seal of the Massachusetts Bay Colony, 1629, unknown artist, source: Wikimedia Commons, http://commons.wikimedia.org/wiki/File:1629_seal_Massachusetts_Bay_Colony_MassachusettsArchives.png, public domain.