I currently live in a big city with lots of crime compared to Japan
That's not saying anything at all. I read an article once that looked at the violent crime rate between the 'safest' area of a US city (Plano, TX, part of Dallas) and the most 'dangerous' area of a Japanese city (somewhere in Osaka), and Japan was still safer.
Several things that you may or may not be aware of:
Job-wise:
- You have half a leg up if you have (or acquire) a spouse visa. Do this before going to Japan if possible. Eventually you can get an Engineer visa "just in case" if you qualify.
- Your ability to find a job really depends on your existing expertise. "IT" is pretty wide-ranging.
- Not having at least business-level Japanese probably excludes you from a minimum of 50% of IT jobs, and if you are outside to Tokyo and maybe Osaka probably more like 90%.
- I always say that speaking English isn't valuable in Japan unless you also speak native or at least fluent Japanese, but that's particularly true in the IT field, where you are competing against everyone else in the English-speaking world for expat jobs that don't require English. Not badmouthing or anything, but it's just a fact of life these days that Indians and others will do the same job for a whole lot less money.
- Unless you are the cream of the crop and/or can land a gig with a foreign company, IT job pay is pretty horrible compared to competitive pay in US cities.
- IT gigs aren't exempt from the overtime lifestyle in Japan.
- Again, depending on your skills and job connections, there's always the chance that you can't find a job and end up teaching English.
Life-wise:
- Hopefully your wife is from one of the bigger cities, because if she grew up on the farm in Sapporo and you suggest moving back to Japan, she's not likely going to have Tokyo in mind.
- I've heard multiple stories of Japanese wives' behaviors changing dramatically when she's back in the family home. Living with/near the in-laws gets weird in any culture.
- Depending on the age of your son, he'll either pick up Japanese super-fast (up till maybe 4-5 years old) or may have some issues, be isolated, etc.
- Kids that speak one language with their friends tend to only want to speak that with their parents, especially if they know their parents understand them.
- Being half-Japanese shouldn't be a big deal in the bigger cities, but if he's going to the school near the farm he might be dealing with some bullying.