Start of october is a bit early for the best diving conditions, season doesn't really begin until november, but you can of course have good diving anyway.
Best diving on Zanzibar: Mnemba Atoll and Leven bank. Spend a couple of days there and then on to Pemba for 3-4 days. There are only a few options on Pemba. My only experience is with Manta Reef Lodge on northern Pemba. I saw that they recieved some bad feedback earlier this year, but I don't know if it is because things has gone seriously downhill very fast, or if the reviewer expected a caribean-style luxury resort?
I was there with my girlfriend end of november last year and we were very pleased. Nice bungalows, good food, helpful staff and the most beatiful location on top of a sandy beach. However the pace is very slow. When not diving, there's not much to do but taking walks in the surroundings (which by the way is very cool), lay on the beach and read, lay in the room and read, play cards ...
The diving was very good with great biodiversity and quantities of both fish and coral. On the contrary to what I heard before going, we had exeptional visibilty with highs in the 50 metre region. Plenty of pelagic speices ranging from big schools of barracuda & jacks, tuna, wahoo. Also big groupers, napoleon wrasse, a few turtles and a huge cowtail ray. Unfortunatelly no sharks or mantas. Perhaps not as spectacular as Sipadan Island or the Sudanese Red Sea, but certainly on par with Similan Islands and the Maldives inmo. The dive center was at that point run by a South African bloke, Elton ..., which was good and tried to arrange what the customers wished to do. I believe the cost was something like USD90 per person/night and then USD30 per dive if you brought your own equipment. Just check current status on their boats - it's cumbersome to get spares and I know they've had trouble keeping their fastest boat running. Transport to some dive sites are long.
There are a cheaper place to stay. In Chake Chake town is a small hotel run by Swahili divers. More backpackerstyle, and I've heard roumors about the dive organisation - that they're not very flexible keeping customers on a leash. Diving prices are probably about the same. Then there's the Fundo Lagoon Resort, but since you're on a budget I guess you can give it a miss.
If you are really only into diving, skip Zanzibar and try to go on a liveaboard like the Jambo. She does 6 day trips, sailing around Pemba. Unsure if there are any scheduled trips in october though. If there are, perhaps you can get a good price if you just give them a call when you're there?
good luck
Christian
