If you're going to take Uber in Boston, be very careful. It's completely unregulated so you don't know who you're getting into a car with. One of the drivers here was recently arrested for raping female passengers -- I don't know if he's still in custody or not.
Although personally I wouldn't risk my life to save a couple bucks, you should be able to get a permit from any police station to carry pepper spray.
There are quite a few 6 AM flights out of BOS so getting to the airport before the T opens is something we've all had to deal with. For me, I just take a taxi and I've always made it.
I hope you'll make it too, no matter what risks you choose.