We are planning on spending the majority of our trip to japan in Tokyo (10 days) with a day trip to Nikko and an overnight trip to Hakone

What is the best option for subway/rail tickets for tokyo?

what is the best option to get to nikko and hakone?

Where can we get currency in adnvance for our trip?

Sorry I can't answer your first questions, but the answer regarding currency is that the best exchange rates are at the bank counters outside the arrival/departure gates at Narita. They are usually within a couple of yen from the market rates. It is also a much simpler process than doing it at a bank.

how about over the internet exchanges which mail it to you before you go??

You can get get some yen from your local AAA office in the U.S.

You can, of course, just get cash from an ATM at Narita.

how about
What is the best option for subway/rail tickets for tokyo?

what is the best option to get to nikko and hakone?

anyone?