I live in NYC & trade a 30-35 minute commute by bike or subway for a lot of savings on rent, but I wouldn't be a happy camper going much further out to save more. I think being relatively central is a worthwhile tradeoff in an expensive city where it costs a lot to live near the core— the price increase to live more centrally isn't nearly as much in more suburban cities, like MMM's metro Denver.
When you say 'take the train', do you mean a commuter train or the subway? Because paying for monthly commuter train passes can eat up a lot of your savings, but a subway pass is more reasonable.
Another consideration is what the social considerations are for you? You sound like you're young and single— is there anyone your age or anywhere to socialize near the $500 neighborhood, versus the $1200 neighborhood?
Also, could you cut that 50 minutes to 35 or 40 with a longboard/scooter/bike/bikeshare pass?
To me, I think, the $1200 neighborhood could be worth it if you could ditch your car (to save insurance) and there are a lot more social opportunities. Otherwise, I would make the commute, or look for a $700-800 neighborhood a bit closer to work but still on the train.
Finally, $3000 net a month sounds like a shockingly low salary (even if your taxes were 50%, which they aren't) for a full-time programmer in a big tech market like Boston— have you checked out the job market lately?