There are two specific details that are needed to determine if you're screwed or not:
1) What is the EI class of service booking code for that specific segment?
2) What does that map to on JetBlue's system?
There is no guarantee that EI J maps to B6 J. ExpertFlyer should be able to tell you what the mapping is or if you call JetBlue back and they still insist you're in economy ask what code they show the booking in on their systems. But I'd start there in trying to resolve the situation.