I agree completely with the above reply - it really depends on where you are going and your tolerance for stopovers. There is no airline that is going to be able to get you everywhere nonstop (though all combined, you can get to most major cities without stopping). I have gone the route of actually having my miles on 2 airlines (DL and US) as they together serve the majority of my destinations. It also means that only AA is left out from my mileage earning.

One thing - the new Terminal A (DL and CO) is amazing compared to Terminal B (US, AA, AC, a few others) and Terminal C (B6, UA). Terminal E (NW and international arrivals) is OK. If you are a stickler for having a nice terminal and/or club, then DL is the way to go (CO only flies to EWR,IAH, and CLE).

If you can tell us a bit more about your common destinations, that would probably enable us to better inform you. Welcome to BOS!