What exactly is your reason for choosing Japan? Meaning do you have friends or family there who you intend on visiting? If that answer is no, I would avoid Japan at all costs with little ones. It is not a really a family friendly destination, especially because your kids are still small. It is also very, very expensive for a family vacation. I would strongly consider somewhere else unless you really enjoy wasting money or you're able to leave your kids with your parents or in-laws while you vacation.