It sounds like you're over 20 and did not take your Japanese nationality.
If you are not a Japanese national I think things will be stricter.
Foreigners trying to get spousal visas when married to Japanese nationals - that alone is usually a process supported by several years of married life in Japan and an impeccable tax payment record.
I don't see your 3-year visa supporting a successful spousal visa application within a 3 month window.
Whatever the folks at the airport say, best result will be a 3 month tourist visa, whether you spill the beans or not. That won't change because shes not Japanese and has no visa, so, tourist visa, that's all she can get at the door.
Whatever you choose to do after that, again, I suspect you will not have the requisites to support her application or that the process will be possible within the timeline you've mentioned, as foreigners in Japan do not typically get visas turned-around like that even when married to true nationals.