I have lived in Japan and lived next door to Thailand so visited many times.
Have a look as to what your after from a holiday as I agree with the others combining them both unless you have lots of time, really does not do either country justice.
They are very very different places to visit and offer very different experiences.
I have never used a tour/travel agent to visit either country, just booked our flights direct with the airlines and then used say in Japan used a booking service called Japan I can, to book accommodation.
www.japanican.com/en/
If you wanting to go down to the beaches of Okinawa, flying is the best way otherwise its a long train journey, flight about 3 hours with plenty all day.
The southern islands are a great place to visit. Hire a car and get out and about for greater flexibility
You may also want to thing about getting a JR pass for the trains which you can only buy outside of Japan by foreigners.
I did look at the costing of tours and some are crazy expensive, but then I just like to do my own thing.
Thailand, even-though is one of my favourite places over the years, is getting more and more expensive.
I could go on, but if you would like more specifics just ask.