I see an itinerary that has a 1 hour 40 minute layover in Lisbon when we fly in from ZRH, to our final destination of JFK. Will that be enough time to go through customs in Lisbon and get on our plane heading to JFK? We'd be going in January.

I have never been through those particular airports, but would never take that short of a connection myself anywhere when Immigrations & Customs are involved.

Why would you be going through customs? Would the two flights be on separate tickets? If they're not, then your bags will be checked through to JFK and all that will happen at LIS is a brief exit passage through immigration as you exit the Schengen visa area. 100 minutes is ample; if you're on TAP for both flights their published minimum connection time (MCT) is 50 - 60 min. depending on flight numbers, but you'll probably be at the departing gate in half that time.

What about a change in Madrid instead of Lisbon with a 1 hour 50 minute layover? It would be on one ticket using Air Nostrum (never heard of it) and Iberia. Would buy it through the Iberia site. Still no need to go through customs?

You clear customs at your final destination; at your connection point you are in transit and do not actually enter the country, but stay airside. You may need to do a passport check, but no customs.1h40 should be fine, and if you are all on one ticket even if you were to be delayed on the first flight enough to miss the second you would be re-accommodated with out charge. In fact, given the more stringent EU regulations, you might even be entitled to compensation in the event of a delay.

>>What about a change in Madrid instead of Lisbon with a 1 hour 50 minute layover? It would be on one ticket using Air Nostrum (never heard of it) and Iberia. Would buy it through the Iberia site. Still no need to go through customs?<<

Customs is totally a non issue. You don't clear Customs exiting. Just like you don't when flying out of the States. Customs is about what you are bringing in, not what you are taking out . . . you won't go through Customs until you get to JFK.

Air Nostrum is the shorthaul subsidiary of Iberia, so the whole process will be seamless. At Madrid you'd have a terminal change (underground train) from Terminal 4 to the Terminal 4 Satellite (T4S) where your JFK flight would depart. The process will be identical to that in Lisbon; you'll go through a very simple passport check as you'll be leaving the Schengen common travel area, but your bags will go straight through. Personally, as a Oneworld traveler, I'd pick Iberia/MAD, but if mileage programs are unimportant to you, then I'd go on budget and timing.

Thanks all for the correction. I just replied to the "go through customs" question w/out thinking if that would actually be happening.

Thanks everyone. We are Oneworld members so we will probably do the Iberia route. Interesting in that when I look for a suitable itinerary on AA.com I find some itineraries with Iberia but not the ones I can get on the Iberia site.
We'd be flying JFK to Mad, then taking Edelweiss (from Seville) to ZRH a week later, and then back to JFK four days after that.