Short answer: either way you just described would be fine

Long answer: Japanese citizens can line up at any line they want, but citizen lines are almost always shorter, so why would any citizen go for other lines (except when the other lines are shorter?) Long term residents has the options of long term resident lines (multiple re-entries visa or permanent resident visa?), but everyone else must be going to the visitor lines.

Now, since you two are a family, the question is can you accompany your wife and line up at the citizen lines instead? That I don't know. Another question is that has any foreigner attempted to line up at the citizen lines to pass the immigration quicker? Can they do it? Has anyone attempted? LOL