O'Sensei's grave is quite out of the way, but I definitely recommend going. It's in the town of Tanabe on the Kii peninsula. You will have to go to Nagoya and change to a local train going down the coast. At the Tanabe train station, you can get a tourist map which will show you the location of the temple where the grave is located. The map is in Japanese, but I think it has drawings which should make it clear. There is also a big statue of O'Sensei at the shore.
Maybe if you stop at Aikikai Honbu, they can give you advice. For an easier trip from Tokyo, you might think about going to the Aiki Shrine in Iwama.