11 days in Japan

Hi!

Now that Japan is finally open to tourists without much restrictions, may I know how can I plan my itinerary wisely in late December with a family of 4 (we have 2 children; one is 5 years old and another is 11 years old)?

Our flights are in Tokyo but we also wish to explore Osaka...

Any advice on affordable family room to stay near JR stations that I can leverage on JR pass?

JR hotels where you may get a discount normally are business hotels. Not really suitable for 2A+2C. Unless you book two separate double rooms.

Probably best to look on a booking website for a hotel.

Try this tool for itinerary suggestion. Enter number of days/nights and region of interest.
https://www.japan-guide.com/e/e2400.html

Tips for traveling with children:
https://www.japan-guide.com/e/e2460.html

When you say traveling in late December, does it include 12/31? If so, you better plan for most places being closed. 1/1 included.

Search on the google map of Tokyo for "hotels", you will see hundreds of results. I would not limit to hotels near a JR train station, as there are many subway lines that are convenient also. You can utilize subway passes instead of JR Pass. For example, use mostly subways in Tokyo and use JR Pass for rest of the country.
https://www.japan-guide.com/e/e2017.html

If you are in Japan 12/31 and 1/1 I would be booking a hotel now. I too am going to Japan in late December to early January (school break) though I am a single adult with 1 12 year old. I have a temporary booking in with one place I can cancel as I debate what I want to do just because those are the trickiest days.

Personally, while I've not stayed there yet, unless you are looking at luxury hotels (i.e. the Shangri-La or Park Hyatt or Four Seasons) I would try looking at the Mimaru chain of apartment hotels. They seem to have quite large rooms with a good set up for 3-4 people. The JR Pass gives you a small discount at the following hotels: https://www.jrhotelgroup.com/en/map.html#kk

I have stayed at some of them and they're not all business hotels, though some are. Some have very large rooms and some don't. I have personally stayed at: The Hotel Metropolitan Nagano, The Tokyo Station Hotel (which is full 12/31), Associa Takayama, and the Visicho in Kyoto.

Also remember to read the New Years section as lots of things are closed on New Years Day. It's one reason we are looking at ski resorts, New Years Day is a very popular ski day!

Good luck!