I lived on the Big Island, Kona side, for a couple years recently. Having lived aboard a boat in Vancouver, BC, I figured that'd be a great way to go there. Couldn't find any space though - the only harbors are man-made, and demand is high. Honokohau Harbor, near where I worked, had a 10 year waiting list for berths. And was definitely not an official live aboard place, but you know how that works.
There is one spot that caught my eye over by Spencer Beach Park, still on the west side of the island - there's a little breakwater built there with some sail boats anchored in it. You can see it in Google Earth - 20° 1'36.46"N 155°49'33.33"W. Not much for facilities. No idea who runs it either. Got in trouble with the locals for kitesurfing there - drifted downwind into the shark heiau. I didn't want to be there either, but luckily I ran into the locals before the sharks.
I also noticed a couple sailboats anchored in the Hilo harbour behind the big breakwater, but I wasn't too interested in that side of the island - too far to commute. I did come across a lot of complaints about the general state of the marinas in Hawaii while I was researching.
Sorry I can't be of more help.