How to tour with JR Pass in Tokyo....

We are visintg Japan in June, have a JR pass. Is it easy (& relativley cheaper) to organise our own tour around Tokyo sights or better to take the Cityrama tour? Also, same query with trip to Nikko? Just feel that if we have the JR pass, may as well make most use of it, rather than spending extra on a bus trip which may take longer and double up travel costs. Also, What is the best additional rail ticket to get to complemen the JR pass when travelling the subways in Tokyo - is it the PASMO? Thankas for your time

Using the JRPass around Tokyo is the least value unless you have extra days left on the pass. Going to Nikko on the pass is ok. But you might consolidate the long distance trip days so you buy the least expensive pass.
The fare around Tokyo is $1.30~$2/ride for JR or Metro. You can take Shitamachi bus (210yen)routes that go around the east Tokyo downtown.
http://www.kotsu.metro.tokyo.jp/english/images/pdf/bus_guide_english.p...

If you're just going to be in Tokyo and Nikko, it would be a HUGE waste of money to get the JR Pass. Local transportation around Tokyo is very cheap on both the local trains and subways.
Don't bother with the JR Pass unless you intend to make a round-trip visit to Kyoto or further.

Sorry should have said getting a 7 day JR pass and will be travelling to Kyoto and miyajima too, then back to tokyo for last 2 days of pass. Is it easy to just use JR pass in tokyo to see the major sites. We only have 2 full days in tokyo - is it better to leave Nikko for another time?

Here are the areas in Tokyo which it is NOT convenient to visit by JR;

- Asakusa
- Odaiba
- Roppongi

Any other tourist areas can be visited easily by JR.