I like TK, NH, and JL.

Look carefully at scheduled departure, connection, and arrival times for this trip.

Looking at the schedules, TK has 2 overnight flights with a brief connection. IST is now great with an amazing lounge. But that routing will be brutal!

NH has a desirable afternoon departure from JFK to HND and an overnight connection! This allows for a break in a great world class city, and affordable, too. Business hotels near HND are a great value.

I'd select NH but select which flights carefully and avoid a bulti-airport connection at TYO.