University/academic jobs do tend to have low pay but do usually have great benefits. The work varies, sometimes super cool sometimes not. It tends to be a mix of people REALLY into what they're working on and people who'd rather not be working at all riding a cushy gig.
Biotech/pharma pays better and if you like the domain can be really cool. The software isn't that much different than the rest of the world for the most part. In most places be prepared to be viewed as a second class citizen as the MDs and PhDs get top billing.
All this said i believe that the bio space is where to be as a software pro in Boston