Hi there
Another alternative is to take the airtrain to Sutphin Blvd, change over to the J train to Canal Street where you can pick up the Fung Wah bus between Bowery Street and Canal Street (china town). Your bus ticket will cost no more than $15 and buses run every 15 mins to 1/2 hour. I have been taking this bus for 4 yrs and have no complaints. Alternatively, you can take the Greyhound bus from Penn Station to Boston South Station.
JFK-Boston