Help needed: Two bestfriends travelling to Japan

First and foremost, if this isn't the correct subreddit, I apologize!

In the summer of 2018, my closest friend and I are planning a trip to Japan. We are planning on staying a month and will probably stay somewhere in Tokyo and do day trips out to other cities. Next summer we'll both be 22, and we are university students. We will be flying out of Toronto, so our currency is CAD$. I had a few questions, and am extremely interested in hearing stories or experiences.

1. Location of rented space: We have been looking at AirBNBs for awhile now; however, we get kind of confused with how important location is when every single place is X minutes away from almost everywhere haha. We want a nice, comfortable place...we don't need a penthouse, but we'd also like a cozy place. We are both 6'4", which may be good information since I've heard things to be rather squishy and small in Japan. So, how important is the location of the space? Is it better to get a nicer, farther place a bit out of the city and subway it...or vice versa?

2. Mode of transportation: I'd assume it is pretty staight forward to use their subways/buses as long as you take your time to plan it when there, but are taxis and subways expensive in Tokyo, because they can get ridiculous in Toronto lol. But I'd assume Uber also dominates over there?

These are mainly our two biggest questions: location and transportation, as all other things we've already looked up in terms of food, attractions etc. These two topics are more dynamic in terms of pricing.

Thank you for the help!