After looking at some tour options, we decided to handle all our own arrangements, and so did a ton of planning. Our main tools:
www.japan-guide.com: this is an excellent resource. Well-designed, comprehensive, easy to use. Includes a good list of cities/regions, and top suggestions on what to see in each. Also covers lodging, tours, how to get places.
The Lonely Planet - Japan (Kindle version): a little more geared to backpackers and budget travelers, but includes lots of information and tips.
Expedia (website and app): this is my go-to travel site generally, and my favorite for hotels. Good selection, good (and sometimes super good) pricing, easy to use, free cancellation, decent guarantees. Very clear on when you have to pay cash at the hotel, etc.
Trivago: this was a new one, recommended by our travel agent friend because it has a filter option for "family rooms." I like this site and will be adding it to my trip planning arsenal. Clean design and easy to use, and the family room filter was super useful. Similar to Kayak, it jumps you to other sites for booking.
Trip Advisor (website and app): good for reviews and recommended things to do. I also like it better than Yelp for restaurant recommendations.
We did sit down with a friend who is a travel agent (and also an advisor for the local high school student exchange program) to discuss some options, and to book flights. Travel agents can sometimes get better deals through consolidators, and we were able to save several hundred dollars on airfare. And we were being a little complicated, as we were bringing Vonn from New York and wanted to coordinate his flight with ours if possible.
Japan is a cash economy, surprisingly. Most hotels, and pretty much all the restaurants, shops, temples, parks, etc. are all cash, all the time. So we made sure we had yen before we left, and also took our Charles Schwab cards (ATM withdrawal fees are waived) to access additional cash. Make sure you know the terms of your cash withdrawals! Note: not all ATMS will take your card. BUT International ATMs are NOT hard to find - all the 7-11s have them. Yes, 7-11s. And they are everywhere.