Lefferts will work for sure. Just keep in mind you'll have less trains at Lefferts....Federal Circle gets (free) trains from both Jamaica and Howard Beach. I think the difference in wait time is only probably going to be like 5-7 minutes (not sure)...but do factor that in.

I don't have any specific experience on the road closures into JFK - but taking the Airtrain approach will destress the situation if not elongating your travels by about 10 to 15 minutes (tops) vs. a no traffic situation.

Keep in mind the walk from the Airtrain for Terminal 5 to the actual terminal is fairly long...so keep that in mind if you are walking challenged.