Stay in Osaka or Kyoto

Hi,
Two of us will be visiting Kyoto and Osaka area in early April 2015. We have a JR Pass. We also like to visit Nara. If time allow, we would also like to go to Okayama for the beautiful garden there. We will be going back to Tokyo after this 2 night stay. We are interest in sightseeing.

Would you please advice which city to stay in.

Thank you.

I hate to say this but I think you cannot book hotels in Osaka, Kyoto and Nara. If you have JR Pass, you might stay in Nagoya.
http://www.japan-guide.com/news/0029.html

As mijiro wrote, cherry blossom season is very crowded in Kansai area. However, depending on the specific date, you might be able to find vacant rooms in Osaka or even in Kyoto. Many rooms are reserved by big travel agencies and they may "release" the rooms before 1 to 2 weeks. Actually I checked some online booking sites and found some rooms in Osaka and even in Kyoto. If you want to book, search for a specific single day since there will be less chance to get continuous 2 vacant nights than a single night. So you may need to stay in hotel A and then the next day hotel B.

In general, Nagoya is less busy.

As far as I searched on "cyberstation"

http://www1.jr.cyberstation.ne.jp/csws/Vacancy.do

there will be vacant seats in Hikari Shinkansen from Nagoya to Kyoto, at 7 o'clock to 8, on 1st to 5th April, which will be the busiest days for sightseeing in Kyoto.

I recommend Kanazawa over Okayama
As the garden is better imo
You could even use Kanazawa as a place to stay as they do have many hotels available. Similar to Osaka station area. Also Kanazawa now has a Shinkansen line direct to Tokyo so it would easy to access.

Stay in Kyoto if possible.
If however due to the Sakura season, prices rocket, use Osaka or some other city. You do have a jr pass to make traveling less of a hassle.

Nagoya has a good mix if cheap (comfortable) and expensive hotels and is not too far from Nara and/or Kyoto.