Aggiemom2020 - my son wasn't in Japan but when he did deploy we used the WhatsApp to communicate. Hopefully someone else will chime in with better info for you though.
My daughter-in-law is from Sasebo, Japan and talks to her family every week. They use an APP called 'LINE'. But you could use others like 'WhatsAPP', DUO, etc. I like DUO.
Your sailor needs to put his U.S. cell phone service on a military hold. Check out how long the hold lasts and how to continue it when it expires. See if he can let you speak for him on the account. My sailor had TMobile and they let him turn on his service when he visited home and put it back on hold when he left.
Your sailor can get a new cell phone and service in Japan. They will help with the contract on base. It is best for him to ask when he gets there. Every new sailor has the same needs. Number one is always the phone.
Let me know if you have any questions about Sasebo and I will ask my daughter-in-law.
My son left Sasebo a little over a year ago now so some of this might be old. I agree with Kim, ask during the orientation. They can probably give current advice. I did ask my son your question and he said that there is a Softbank kiosk on base so that is really easy. Softbank only has iPhones (or did as of a year ago). My kid wanted an android phone and lived off base so he went with AU which he got in town. Data on the plans is limited there and expensive (his words, I don't know how it compares). As he was leaving Japan, AU started offering an unlimited plan again. No idea again how the price compares. If your son will have access to wifi reguarly, he may not need much in the way of actual data. You might also see if his phone is unlocked or could be unlocked. He might be able to just use his phone and get a local sim card. My son and his GF said that was possible but I thought that Japan was particular about using overseas electronics long term in Japan. So I wouldn't count on that, just a backup plan if he has a phone he likes and wants to investigate that option when he gets there. Having his US phone work for a few days when he first gets here is a nice backup in case he needs to reach out to someone regarding the bus from the airport to Sasebo, etc. We activated pay by the day (if he used it, was $10 for the next 24 hours or something like that) rather than buying a ~30 day international plan ahead of time. In the end, I think he needed to use it 1 day, cheaper than the 30 day plan. That was on ATT.
Whatsapp, Facetime (iphone), Facebook Messenger, Duo should all work for chatting and messenging. So nice to have options.
We visited our son in the fall of 2019. Traveling from Toyko to Sasebo via train for a week. We then spent another week in Sasebo. What a beautiful place. The farther south, the more green and beautiful it seem to get. Best of luck to your son!