I agree with adambrau, having had similar experiences on this route very often. My policies:
a) JFK is the best of the airports in general before 6pm
b) Avoid Mesa
c) At the first sign of delay, call and get protected to your final destination
d) If your final destination is not transcon (like ORD or MSP) then JFK is *bad* because your protection options are not good.
e) Know the alternative airline options (JetBlue, etc) to your destination JIC you need to find an alternate path to your destination
f) Check the *inbound* flight status over and over again. You can easily figure out which aircraft is operating your flight INTO JFK (because UA only flies from IAD-JFK) and that flight's status will be more accurate than yours. Really. Don't count on UA/UX to update flight status in real-time, they won't. The more leadtime you have, the better.
g) Don't be afraid to change airports between LGA and JFK if you find that a situation has degraded. They are only 15 mins apart (and $20 cab ride). You need to call and find out what the situation is with the alternate flight at LGA and keep your finger on the pulse of it by calling/checking online repeatedly.
Yes, I know it sounds neurotic - but it's the only way to take control of your destiny (used lightly) when UA/UX won't really help.
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