Two of us are going on a short trip to Japan (4 1/2 days) in the second half of May. I wonder if we can do both Tokyo and Kyoto or would this be stretching it too thin? Second question is, it seems that the last train/bus from Narita to Tokyo leaves at 21:45. Is this correct? We arrive at 21:35, so obviously we won't make it. What are the other (affordable) options for ground transportation? Thanks for all your help.

That is pushing it, but it really does depend on where you are coming from. If you are arriving in Tokyo after a long flight and time zone change that is one thing. If you are arriving from Seoul or Taipei, then it is a bit more reasonable. Shinkansen or air travel would cost about $250 each.

Yes 4 1/2 days is too short for Tokyo and Kyoto. 4 1/2 days is too short for Tokyo alone! I would stick to Old Edo and visit some of the many historic and cultural sites in the city: Sensoji Temple (Asakusa), Meiji Jingu Shrine (Harajuku), Imperial Palace (Tokyo Station), etc. When you've seen one temple too many, you can check out: Shopper's Paradise (Ginza), the Red Light District (Kabukicho in Shinjuku), the Electronic district (Akihabara), Teenybopper Central (Shibuya/Harajuku), and Tokyo (man-made) Bay (Odaiba). Tokyo is a great mix of the old and the new. There is definitely a lot to see and do in Tokyo alone. As for the train, there *should* be a later train. (I believe the Keisei Skyliner which goes to Ueno, runs later than the Narita Express.)

For second question.

The last train/bus leaves Narita around 23:00. Don't worry!
( Trains may last earlier.)

For detailed infromation, please try this link. You will find "Transprotation Guide" , and can serch rail and bus timetables in English.

http://www.narita-airport.or.jp/airport_e/index.html

And I think it is too short to visit 2 cities, too!

Last JR train (rapid) leaves Narita terminal 1 at 2217 and terminal 2 at 2220. Last Keisei train (limited express) departs terminal 1 at 2243 and terminal 2 at 2244 (Narita Express and Skyliner finish earlier). And there are limousine buses to various destinations in Central Tokyo up to 2300 (Tokyo City Air Terminal and JR Tokyo).

Thanks everyone for good advice. Your help is very much appreciated. I think we'll just stick to Tokyo and enjoy it fully. We will be arriving from Hong Kong so it's not too bad in terms of flight duration. I'm looking at Sawanoya Ryokan in Ueno as the most attractive option to stay, given the location (museums, parks, etc.). Best Regards.