Going to Tokyo, Osaka and Kyoto mid May for two weeks. Looking for recommendations on areas to stay and hotels that are nice. Any help would be appreciated. Thanks

Stay in Shinjuku in Tokyo and visit Shibuya.
Stay in Dotonbori Shinsaibashi area in Osaka.

Tokyo we stayed at New Otani as a blind hotwire. I can highly recommend the Imperial Hotel chain. Try Imperial Osaka.

Washington Hotel Shinjuku has airport limosine bus service, so you can get there directly from Haneda without having to switch to different subways or walking up and down flights of stairs with potentially heavy luggage. Shinjuku is great for night life as well.

Stayed at Ibis Shinjuku. Great location/price and great hotel.

My brother and I stayed at Hotel Gran Ms Kyoto. It was reasonably priced (booked through booking.com) and quite nice. Easy to get to with public transit and in a good part of town.

The nice thing in Japan is that even the inexpensive hotels are clean and well run.
Honestly go with whatever is in your budget and whatever is most convenient to where you want to explore. You can look at pics and see what the decor is like. The decor, amenities and space are the only things that vary. Service and cleanliness is stellar in all of them.
North American chains are very expensive, more inexpensive premium local brands are just as nice and substantially cheaper.
I’ve stayed at GrandBell when I was in Shinjuku and it was a very nice space. I’ve also stayed at APA in Shinjuku etc and they are really nice as well.
(Apa take over existing hotels and don’t really have a corporate theme in the hotel so they vary widely in their appearance and amenities) but are mostly budget friendly well run hotels.
Keep in mind that rooms are much smaller in Tokyo than the rest of the country.
Tokyo is a massive place and if you want to do more than one section I’d dedicate at least a week of your two week stay there.
Osaka can be a three day adventure as can Kyoto.

Also I recommend downloading Agoda to book your Japanese hotels.
They seem to have a much wider selection and better deals on places there than expedia/hotwire do.

Also if if you are flying into Haneda you might want to just take a cab to Shinjuku as it’s only a $40-50 ride and not worth navigating a very complex public transit system in a foreign language right after long flight.
Most of my Tokyo bound flights are into Narita. In that case take the NEX (narita express) to get you to Shinjuku station, where you can take an cab to your hotel.
*don’t think about taking a cab from Narita to Shinjuku (or any part of Tokyo you want to stay in) as it’s going to be a $300 cab ride and take hours.

Closer to $100 from Haneda to Shinjuku
There is a bus that does the same route for $15

uber from Haneda to Nihonbashi area was ~$80 last March when I went for cherry blossoms.. much easier and cheaper to take the subway unless you have giant bags.

We stayed at the Sheraton Grande Tokyo Bay in 2015. It was a bit pricey; but insanely nice. Its one of the Tokyo Disneyland hotels so it's a bit out of the way (you'd have to take the monorail to and from the hotel to get into the heart of Tokyo).

Check before you go because my neighbour just cancelled his trip this week because a lot of tourist attractions are closed because of COVID-19 fear.

We stayed at Conrad Tokyo and it was amazing!

Tokyo is insanely expensive to get around in. Its better to spend a bit more on accommodation in an area you want to explore, then get around by subway. air bnb is also great there, enjoy!

For something to do, check out Japan Foods'n Booze. Manami offers different experiences in the Oiso area.

Good advice from Wendy

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Following

A more budget friendly option is the Red Roof Inn and Suites in Osaka, great location. Close to two different subway lines (not JR though). Close to Kuromon market and walking distance to Dontonburi. Small rooms but not as small as APA. APA in Ikubukuro Tokyo I had a bad experience. Look into the Japan Travel Planning Group
I did day trips from Osaka to Kyoto but wish I did it the other way around. Wish I had more time in Kyoto, it was my favourite

Mindy I totally agree with this. I did the same and regret it. Kyoto needs two full days

In Tokyo, I always recommend Memory Lane in Shinjuku - 1 Chome-2 Nishishinjuku, Shinjuku City, Tokyo 160-0023, Japan

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Sasha S

Is it safe to go to Japan this time? I’m suppose to go in 2 weeks and still having a second thoughts