Hi and welcome to GMAT Club!

Non profit is a tough industry (to be honest). There are not that many MBA-level jobs that require or are able to support someone pursuing this track. Graduating with $200K in debt, and your classmates making $150k+ you will be looking, at best, at an 80K job, if you are lucky. This does not stop many of course, or most folks pursuing non-profit field but it does help quite a bit in admissions and subsequent recruiting if you have a clear path/target as to what non-profit you want to pursue, if they recruit out of BSchool and if they have positions that you could count on. Sometimes, VP's retire from Amazon and Microsoft and work at those places for pennies or just for fun. My aunt is doing exactly that and "consulting" for one of the non-profits, not getting paid a whole lot but she is at a diff stage in her career and this is just something to do. Anyway, all of this is addressed if you have a clear target and it can be done and bschools buy into it.

About experience and GMAT scores, 3 years is fine for consulting. Many people go after 3 from MBB's and not a concern. If you can improve GRE, that would be nice but I feel you could have a good enough score for at least some programs. TOEFL - don't bother, it is pass fail and nobody looks at your scores. I had a perfect TOEFL score and nobody ever mentioned anything about it.

Good luck!!!

Non profit after MBA is a tough deal to manage as @bb mentioned above, however, it will be important to have clarity as to where you are headed and why you need an MBA for that. Another point - for the GRE - atleast 330/332 plus is a good score to go with.

As already mentioned above the non-profit space has it own set of challenges both in terms of compensation and career progressions. Typically we have seen tons of candidates leverage their MBA to transition out of the non-profit space into corporate roles. If you are clear about pursuing a full time career in the non-profit space, do consider that if it is personally satisfying to you, at the end of the day what matters most is what makes you happy. No point doing a conventional banking / consulting gig only to end up hating yourself, plus there are ample avenues nowdays to amplify your work and gain substantial traction. Noted that you are from Japan and my sense is that the non-profit is typically not open for international students and hence you can probably leverage the 3 year OPT to work in the industry but will eventually have to leave the country if your employer doesn't sponsor your visa. The broad trend is that larger firms are more open to sponsoring your visa as they have the resources, non-profit guys are smaller players and hence will be hesitant. B school adcoms are well aware of these intricacies as there is a strong feedback loop with the career services team and hence they will factor issue into your final decision.
In terms of candidacy 4 years by the time you head to your program is typically a sweet spot, the GRE maybe slightly below median for the schools that you have considered.
Do factor in the above observations prior to taking a final call to applying to the schools mentioned.

All the best for your GRE!!