My son is taking a brief trip to Japan during college break. In terms of his flight, please let me know if you have any suggestions or thoughts about this plan. We live in Philadelphia. He would fly out of JFK or Newark on Friday, morning Nov 25th. He is only able to stay in Tokyo until the following Friday (the day after Thanksgiving) the 25th. With that in mind, I'm thinking a direct flight makes sense. Wondering if leaving from JFK or Newark would be the better option on Friday morning since it's pre holiday week. Additionally, I'm thinking that upon return, he could return to JFK and stay at a hotel that night and return to Phila by train on Saturday. Lastly, a) are their any airlines that might be best to use for this trip and b) should be obtain travel insurance for trip cancellation/schedule change? Many thanks!

oops, he would be flying out on Fri, Nov 18th in the am and leaving return flight from Tokyo on Friday, the 25th in the early evening.

Assuming he's going to be in NYC in the first place (and not in Philly) for the departing flight, I'd recommend Japan Airlines' nonstop from JFK to Narita (also sold by American as an AA "codeshare" flight, but operated by JAL.) The reason is that it's on a 787, and the more comfortable air pressure and bigger windows on 787s can really help on super-long flights.

Coming back, you might look at an "open-jaw" itinerary, where he clears immigration and customs somewhere in the US, then changes planes and flies right into PHL. These are easy to book - look for "multi-flight" options (or something similarly worded) on airline or online travel agency (e.g. Expedia) sites. An open-jaw ticket is usually priced similarly to a round trip, and any difference between a NYC-TYO-NYC ticket and a NYC-TYO-PHL one would probably be less than the cost of the hotel + train option from JFK to Philly. Besides, the hotels near JFK are uniformly terrible, and NYC hotels at Thanskgiving, particularly on Black Friday, are eye-watering expensive.

I would not bother with insurance; there are lots of alternative routes/flights that the airline use in case of irregular operations.

From Philly, going to JFK is a much more arduous and time consuming than EWR. In fact, if he's really starting from Philly, a connection via ORD or elsewhere is probably preferred over the trek to JFK.

Also, if he plans to split his time between Tokyo and Kyoto, it might make sense to consider flying into one city and out of the other. For Kyoto, Kansai is a good choice.
http://www.japan-guide.com/e/e2034.html

Fantastic, helpful feedback. Thank you all so much. Any additional thoughts/suggestions feel free to post.

Most importantly: He should spend LOTS of time with japan-guide.com, the single best source of information on traveling to Japan.

I think you mean that the departure date is Nov 18 and return is the 25th.

You could use these "All Airports" options in a fare search.
TYO for Tokyo Haneda or Narita airports
OSA for Osaka Kansai or Itami
NYC for New York JFK or Newark

Nov 23 will be a Japanese national holiday, Labor Thanksgiving Day