There are lots of affordable accomodations in Honolulu and huge differences in Quality as well, what is your price target?
My suggestion on the Big Island (Kona) is the King Kamehameha Hotel which I think is run by Outrigger. It is very well located in Kona and I believe it was recently refurbished. It is located on the beach where they start the Ironman competition.
I've never stayed in Hilo, and I'm not sure that I would stay in both Kona and Hilo on the big Island. Hilo is the less expensive option but as it is the "wet" side of the island, most visitors tend to stay on the Kona side and drive over to Hilo for the day, It is an interesting place and has a much more "old Hawaii" feel to it then Kona.
[This message has been edited by Leisuremiles (edited 07-24-2001).]