If all 3 kids are truly under 2, then it does not matter as mentioned above.
If only one is under 2, and the others older, then its about mapping out kid activities.
I've visited both countries.
Japan is a great cultural experience. Ive been to Tokyo Disney, and would recommend 6-7+ for this.
In Italy, there is Gardaland, which I took my 10 and 13 year old to. This has a range of activities, however has a number of roller coasters, similar to 6 flags in the USA. It has a peppa pig land a a section for smaller kids, but probably not worth the visit.
The real consideration is what is the adults wanting to see and do, and can they do this in either country, whilst with a pram/stroller, or do they need other arrangements.
In Japan, I walked a lot in Kyoto and Tokyo.
In Italy, we walked even more.
So in summary, choose your country for your adults, and then plan strategies to entertain, or make the kids trip enjoyable.