I fly both regularly. Briefly...
Advantages of Virgin:
- Order food from your seat
- More reliable from Boston (JetBlue is chronically off schedule in Boston)
- Nice first class option which you can upgrade into for reasonable prices if you get very lucky
- Food offered is better than JetBlue
- Bad but somewhat usable Wifi on every flight
Advantages of JetBlue:
- Regular coach seats have much more legroom
- Even More Space seats are readily available and inexpensive; there is only one coach exit row with extra space on most Virgin planes, and Main Cabin Select, which has about the same amount of space as an Even More Space seat, is much more expensive most of the time.
- Free snacks
- Much better wifi but no guarantee it will be on your flight
For me, I am currently choosing Virgin over JetBlue for BOS-SFO, but as soon as JetBlue finishes installing wifi on all its planes, I will be switching. The upgrades on Virgin are nice but just too hard to get (maybe 1 of 10 flights for me, even with status).