Looking for a hotel in Tokyo can be overwhelming just because of the sheer amount of choices and the vast size of the city! Which part should I stay? Which hotels are good? those are the questions that I get asked ALL THE TIME so here's my recommendation!
Omotesando is my favorite area because its central; close to many of the tourist sites; super quaint, surrounded by shops; nearby to my favorite restaurants - but there are almost no hotels there. So... what I do is to look for AirBnB closish to Omotesando station. Alternatively, there is TRUNK HOTEL - a new concept hotel! It's not 5 star luxe hotel but it has all that you need and the location is AMAZZZING!
Shibuya is probably the second place I'd recommend for tourists although I'd personally never stay there because its toooo hectic but ... as a tourist it's a good option because you are in the middle of the action! There aren't great hotel options here either :( I guess the best one is Cerulean Towers - its a bit businessy and its large. No cuteness but its practical!
Ginza is where all the fancy 5 star hotels are lined up. So if that's your priority, go there! I personally find the location a bit out of the way from the actions in Tokyo but it is close to many shops, restaurants. I guess its like staying on 5th avenue, definitely not SOHO! You'll find AMAN, PENINSULA, MANDARIN, FOUR SEASONS etc etc.. I've stayed at PALACE HOTEL few times because its cheaper than the rest but the quality is still great! And their breakfast is better than any others! If I have to choose from all the others, I would go with Peninsula 'cause its connected to the subway - which should be your mode of transportation in Tokyo!
Roppongi is .... messy and dirty, full of foreigners and expats but it is close to everywhere you'd want to go. There is RITZ and GRAND HYATT here and they are super nice! They are both connected to a mall - Midtown and Roppongi hills respectively so if you like beautiful malls, and don't mind being amongst expats, Roppongi is a great option because it's super central!
Akasaka is a business district... and it has no charm. But there is one of my favorite hotel - TOKYU CAPITOL. It's high-end with a taste of Japaneseness. And Akasaka is close to many things as well!
Shinjuku is another business district but it also has a great shopping area, and nice bar area called Golden Gai so it's definitely worth visiting while you are in Tokyo. Most importantly, this is where the famous PARK HYATT is..and I suggest everybody to visit the fantastic bar! great vibe, great drink, great crowd. It's awesome! And while I absolutely LOVE this hotel, its just too far from everything! Even from the Shinjuku station. So unless you are in love with the movie "Lost in translation" I suggest you to opt this option.
And if luxury is not something you need, you should definitely consider APA HOTEL - it's a chain of hotels and there are many in Tokyo so you can choose the one closest to the area you like. It's a business-like hotel and the rooms are tiny but they are convenient for sure!
CONCLUSION
My recommendation is AirBnB or TRUNK if you don't need the 5 star service. If you need that, either the RITZ or GRAND HYATT in Roppongi or PALACE / PENINSULA in Ginza! Good luck!
And if you are wondering what you are going to do at night in Tokyo, check out my friend's recommendation here!!