You can do it online as long as you purchase your JR pass from the official JR-operated websites (https://japanrailpass.net/en/ -> https://www.japanrailpass-reservation.net/), and not through any of the third-party authorized resellers (e.g. jrpass.com, which appears to have won the SEO game). I was able to book tickets on specific trains online quite conveniently through the same website that I purchased the pass. While I still needed to go to a kiosk to print out tickets, I feel like I reaped the benefits of it by being able to snag windows seats early on a few scenic yet nearly full trains.
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