Since I get this question a LOT, I made a blog post about it.
Access: 50 minutes via limousine airport bus from the airport. Take the bus bound for Osaka Nanko for JPY1,550 per person. The first bus departs at 09:10am and the last bus departs at 9:10pm.
It’s pretty close to Universal Studios Japan and this hotel offers free shuttle to go there. I’ve stayed here a couple of times and each stay has really been awesome! They also have free shuttle services from the hotel to Osaka station, very convenient I must say!
(Photo courtesy of Hyatt Regency Osaka)
Narita Excel Hotel Tokyu
Access: 10 minutes by taxi from Narita Airport, Keisei Narita Station and JR Narita Station
15 minutes by Hotel’s free shuttle bus from Narita Airport Terminal 1 & 2, and Keisei Narita Station(Comfort Hotel side)
* I don’t really suggest staying in Narita unless you just have to be closer to the airport. It’s pretty far from the city, around 1 hour train ride to go to Tokyo. I’ve also stayed here a couple of times though I don’t really loved the amenities, it’s budget friendly!
Access: 3 minutes walk from Shibuya Station
Shopping, night life and more! Although I haven’t stayed here (I’m a local), I’ve heard really good recommendations about this hotel. Aside from the chance to stay in the heart of Shibuya, what else should you look for? Shibuya 109 and Shibuya Crossing are only 2 minutes walk away!
Kyoto Tokyu Hotel
Access: 10 minutes via hotel’s shuttle bus from Kyoto station
My friends stayed here and I thought it’s pretty good one! Although he said that the bed was not that soft. Maybe some people like it that way? Anyway if there’s a place in Japan that you shouldn’t blink at all, it’s Kyoto.
Disclaimer: I’m not an hotel expert since I live here but hope this helps.