@Adam Wells
I will paraphrase what I think your question is, because I'm not positive I understand: "Should you invest in Boston because eventually appreciation will be more, or should you invest in New Bedford where you will have higher cash flow and less appreciation?" (Is that correct?)
For starters I don't know NB, however, I imagine it's no different than most major MSA's and secondary or tertiary markets.
A few questions to ask yourself:
1) What are your financial goals? Given the choice of one or the other, do you prefer to buy a place that in 20+ years from now will be paid off and will be your source of retirement but not much income now, or buy a place now that will cash flow but will not appreciate so much down the line? (This probably doesn't answer your question, but it's a personal decision.)
2) Where do you think the Boston market is headed in the next 5 years? Many investors are predicting a correction in the major MSA's, that may not apply to Boston at all. However, if you think Boston will see a correction soon, maybe it makes sense to invest in a cash flowing area now and use that money to buy in Boston when (if) prices come down.
3) How management intensive is it to invest in NB? Is it low class? If yes, you might not want the headache of it, and prefer the Class A tenants in Boston. Or maybe you prefer to put in the work and plow through the headaches to make the extra return. It's really a personal decision and there's no right or wrong answer across the board.
Good luck in whatever you decide!