I think you should go with your gut, you said you gut feeling was to run with the offer I would say do it. Everyone I know who works for JetBlue absolutely loves it, and won't be going anywhere else. Either way its a roll of the dice, its a gamble to stay and wait to flow just as much as it is to progress your career and go with JetBlue. If you could drive to work, I don't think you would ever regret it.
Also, lets assume things stay constant and assume a four year upgrade at B6 or a 4-5 year flow to AA as you stated. In four years at B6 you would be a junior capt, making around 189 a hour, and able to sell back 9.5 hours a month at 1.5% or an extra 32,319 on top of your base salary! Or you hang out at envoy, wait for the flow and make 80ish per hour on reserve at AA the same year you could be making around 200k at JetBlue at min guarantee and PTO sell back. The icing on the cake would be driving to work.
To me its a no brainer, run to JetBlue. In full discloser I left envoy to start at an ULCC after 2 years and 10 months. Good luck to you!