No question given the two choices I would choose UAL.
I am former UAL (I did not accept recall because I found a great Part 91 gig) and I have friends at both UAL and JB. The JB guys are not optimistic about the situation going forward and a few are looking at other gigs. The UAL guys are a bit uncertain about UAL's strategic plan (or lack thereof) but they are not bailing out yet. Two of my UAL friends just transitioned to the 777 fleet and they are very happy with their schedules/layovers after years on the 300/500 and Airbus.
If you go to JB, you will have to fly into and out of JFK for at least awhile - and that is a complete nightmare. I can't imagine flying into that mess multiple times per day. On top of that, you would have to live with the uncertainty surrounding JB's future in a very difficult, low-cost environment. DAL is intent on pounding it into the ground at JFK while other lower-cost upstart airlines like Virgin America and Skybus continue to lower fares and reduce JB's margins on some key routes. The low-cost carriers will impact all airlines including UAL, but other LCCs with huge aircraft orders (Air Tran has 50+ 737-700s on order, Spirit has 30-40 A319s on order and SWA has 100+ 737-700s on order) will have to put their new airplanes somewhere, and any successful route for JB will likely be targeted (resulting in lower margins for all). The LCC industry will become a blood-bath and consolidation could very well happen in the next few years (and merging seniority lists will be fun - just look at USAirways/AWA).
Sure, this decision could be a crap shoot. UAL could very well merge with someone soon too. However, I doubt that the Department of Justice will allow a big merger that would result in fewer consumer choices. The Delta/USAirways merger would have never happened because of overlapping hubs/routes that would have required consolidation and fewer choices for consumers in some markets. I think a big merger would only be allowed if liquidation were IMMINENT and thousands of jobs were at stake (USAirways/AWA) and hubs were not overlapping. So, Tilton can continue to look for merger partners, but a partner that fits the bill might not materialize... I think UAL offers fewer risks than JB - plus, you can fly international routes (beyond Cancun and the Caribbean) and someday fly bigger equipment like the 777 and 747-400 if you ever have the desire - it would be nice to at least have that choice.
I'd choose UAL. That's my $0.02.