If honeymoon - better go on your own, DIY. You'll have all the time by yourself and no need to follow tour's schedule.
Japan is pretty easy to travel. It's also muslim friendly. You can find prayer room in the train station as well in some dept store. Just study the 'japan travel"
I've been to Japan 6 times and all without using travel agent.

If you're going for snow- you can go to Hokkaido. I've bee to Hokkaido twice ie during summer for lavender and end Dec for snow.
Tokyo is much like other metropolitan cites, busy city.

You can search also at this forum -'https://b.cari.com.my/forum.php'. Go to pelancongan and search for 'All About Japan".

Good luck