You can make reservations at any JR station in Japan. I am not sure, but I don't think that the train books out very often outside of the peak travel seasons. In the worst case, you can ride by unreserved seat.

If I have a sister in Japan, can she book the seat for me without payment because I will use my JR pass.

No, an activated Japan Rail Pass is required to make free reservations.

I will buy JR 7 days pass , in the last day I would like to take Akebono train from Aomori to Ueno. This train will arrive in the eight day, will I have to pay extras?

If I can not book that train before I fly, which website I can check an available berth?

The following website lets you look up seat availability, but it does not seem to be able to display the complete information about night trains:
http://www.jr.cyberstation.ne.jp/vacancy/Vacancy.html

Does JR pass cover JR bus from Samani - Erimomisaki in Hokkaido.

In case you can only read English (because I know Chinese and therefore I can recognise some of the Japanese characters on that page), this is already the page showing the seat vacanies for Hamanasu express. Unfornately, this is provided by JR Hokkaido and therefore can only show you the trains from Sapporo to Aomori, but not the other way round.

Anyway, my personal experience, I have used this train last summer. I made the booking only 1 day before I take the train and I can easily reserve a seat with my JR pass.