The short answer would be no...
Now I don't know if this is written in the rules anywhere but unless an agency explicitly indicates women customers (or couples) are OK, they generally are not. NHP may be friendly towards foreigners but there are limitations and I could pretty much guarantee you'll be shown the door the moment you arrive.
Having said all that, there are some places/providers in Tokyo that are indeed okay with couples. It's more expensive than say NHP but also a much more intimate, better quality experience in the comfort of a nice room or love hotel.