I'd like to know the answer to this question myself. Meanwhile, along with some of the other route finders I have mainly been using JR West's timetable and route finder to quickly look up routings (and to see fares), because I like the way it works and because it covers nearly all of the trains I will be using on an upcoming trip. It will give you the price of an itinerary with green seats or regular seats. It actually does cover more than just JR West trains (for example, it does a good job for Kyushu and Shikoku), but isn't particularly great for JR East territory (although it still finds a lot of routes and fares). I used it to do my own calculations that determined that a 3-week nationwide green pass is without question the best option for me, for my next trip. I could have a fun trip with other transportation solutions, but the trip I have planned with the JR green pass is (for ME) the bee's knees... Of course, for some people, green-car travel is an extravagance that they can't seriously consider (or don't wish to), whether it is with a pass or with point-to-point tickets. At any rate, to this point I haven't found anything better than the JR West tool for finding green-car options and prices, recognizing that it isn't a perfect or total solution:
https://www.westjr.co.jp/global/en/timetable/My sense is that if a pass calculator tells you that an ordinary pass will pay off for ordinary class travel, then probably a green pass will pay off for an itinerary where you are able to use green cars for most of the trains. But you have to be careful, because a lot of the limited express trains have no green cars, and some shinkansen trains have no green cars or only a very small number of green seats. You also need to remember that green cars always require reservations, which some people find onerous. (However, if you buy the pass from the official site, you can make, change, and cancel reservations online, which is not onerous.) Also, I booking seats for my upcoming trip using my three-week green pass (wheeee!) I found that some of the green cars had very few seats available even though I booked at the very earliest time I could (a month in advance, from 10 a.m. Japan time). It would be very annoying to pay for a green pass and then find a lot of the cars sold out when you went to book.
I haven't found anything simple that can tell you whether a green pass will pay off. But I will say that for some people the nationwide pass (green or ordinary) is still a good deal, and you definitely don't need to make long-distance trips constantly to get it to "pay off." (It was easier for me to get a three-week nationwide pass to pay off compared to point-to-point tickets, a one-week pass plus other solutions, or a two-nationwide pass (which was not a good solution at all). I was sorely tempted by some of the regional passes that let you ride the Nozomi and Mizuho trains, but in the end the plain old nationwide pass, which covers Tokyo to Osaka on the Tokaido shinkansen, was the best choice for me). I fully understand that for most people, none of the nationwide passes will save them money these days, and for many people any passes will be far more expensive than the alternatives.
I also use JR Cyber Station a lot. Its main function is to indicate seat availability on limited express and shinkansen trains, but what I use it for is mainly to identify limited express trains on short-distance urban runs (like Osaka Station to Shin-Osaka Station, Kyoto Station to Osaka Station, or Yokohama Station to Tokyo Station) and to identify trains that simply HAVE green cars, as well as to gauge the likelihood that I will be able to reserve a seat when the time comes. Once you understand the ins and outs of using it, and what it can and cannot do, it is a very valuable online resource.
https://www.jr.cyberstation.ne.jp/index_en.html