What is the best way to travel in tokyo for 6 days, Kyuto 3 days, and Osaka 2 days? rail pass or ticket?

I returned from tokyo and osaka yesterday... if you are flying into and out of tokyo, then the JR railpass is worth it. It was about $245 for a 7-day pass last week... the price fluctuate depending on the exchange rate... you don't have to pay for the 'green car'... the 'ordinary' car is perfectly suitable... there are non-smoking cars in both categories... if that's a requirement... the JR pass pays for itself if you plan on taking the shinkansen (bullet train) on multiple long distances... the tokyo-shin osaka route is about $140/one-way. The osaka-kyoto trip is about $14/one-way... the extra benefit is that the JR pass is good on the Narita Express from the airport to downtown tokyo.... about $30 value each way... the pass may be well worth it for the time savings at the rail station trying to figure out each route, schedule, and price and if you expect a language barrier then it's most likely worth it... all you have to do is display your pass each time you pass through gates... (you have to exchange your voucher for the actual pass once you arrive in Japan... very easy and straight forward)... sounds like your trip will extend past a 7-day visit period... you can always get the 14-day pass though... you can make seat reservations for free with the pass.... I might recommend that you get a pass and stay in osaka and make day trips to kyoto... that way you only unpack once... one more thing, the pass is good for all the other JR lines as well, which you'll take in tokyo and elsewhere... anywhere from about $1.50-2.50/ride... beware though, you'll want to take subway rides as well... and these will cost you in addition to the JR pass... the subway and JR rail are two different companies... the subways are about $1.80-2.50/ride... do your best to figure out your routing and price out the individual legs vs. the pass... if it's close, go with the pass...

I would suggest you to get a Japan Rail (JR) Pass valid for 7 days. I got it 2 years ago for 37,800 yen, and with that I could travel on the Green Car (something like the first class coach equivalent) and on all JR lines. I assume that you will spend the first 6 days in Tokyo, then only you will travel to Kyoto and later on to Osaka. the Tokyo-shin Osaka return fare on Shinkansen is very expensive. Since you're going to spend a total of 5 days in Osaka and Kyoto, it might be a good idea to start using the rail pass the day before traveling to Kyoto, so that until the day you leave Japan, it will be exactly 7 days and the rail pass will have been utilized to the fullest.