I dived Southern Leyte in August '02 and it was really good. Unfortunately I was not there during whale shark season (which is Jan-Jun I think) but I enjoyed the diving. The reefs are in great shape (which is not always the case in the Philippines).
The best dive resort to use is Peter's Dive Resort,
http://www.whaleofadive.com/ie/index.html. Peter is an Australian married to a Filipina. Their operation is a little basic, but they really care about the environment and treat their customers well. They have a few rooms and cottages for guest.
Enjoy the diving.
Drew