Based on your travel I'd get a RailPass. It may seem like a bit of Cash upfront (300$ roughly/pp for 7 days) it's a good deal when you figure that it will

A.) Cover your train ticket from Narita to Tokyo (Narita Express)
B.) Cover any travel in Tokyo that you take on a JR line (Which is pretty much any non-subway line), either train or bus.
C.) Cover your shinkansen/train travel between Tokyo/Osaka/Kyoto

When you get to Kyoto you can purchase a one day pass for roughly 5/6$ that covers buses and trains.

As far as hotels, I would look into business hotels. They're a better deal than most hotels. I've never paid more than 95$ a night in Tokyo.