I'm not sure as tot he probability of both getting in but it has been suggested that foreigners have higher chance of being accepted than japanese runners. It may be because the Tokyo marathon wants to increase it's global appeal.
No harm in both putting in an application I think you only pay once you're accepted so if one didn't get in the other would not lose out.
Plenty of accommodation and flights so no real need to rush to book however if you both get in it might be wise to book your pre-marathon accommodation early.
I posted a detailed blog of the marathon further up to give you a flavour. Tokyo is certainly worth the trip.
Autumn marathon plans now finalised and Frankfurt is the marathon of choice. I last did this race in 2013. Flights, transport to the city and accommodation are all reasonably priced with decent choice.
After the race in 2013 we walked into a Bar, received a round of applause from the locals and a round of free drinks. What's not to like.