Marie E. Daly is an expert on researching Irish ancestors in Boston and Massachusetts. The New England Historic Genealogical Society has an article that she wrote with the title 'Identifying the Origin of Your Irish Immigrant Ancestor.' 
Some of the links might not work due to the age of the article but it contains a wealth of information on the topic the author writes about. Daly discusses immigration and naturalization records, passenger arrival and departure lists, tombstone inscriptions, newspapers, business records, and other records.
You can read the article here.
 Daly, Marie E. Identifying the Origin of Your Irish Immigrant Ancestor. 22 May 2000. Available online at http://www.americanancestors.org/identifying-origin-your-irish-immigrant-ancestor : accessed 2 January 2014.