Depends what you are looking for.
We favour Manado-side because we also like to go into town, go up volcanoes, go to Tangkoko National Park (tarsier monkeys, black macacques, hornbills etc etc), go to Tomohon up in the highlands to the market, do scenery etc
as well as
diving walls (Bunaken island)
and doing macro/muck critters etc (Manado-side Poh-Poh and lumbalumba jetty)
We are happy to chill out on the boat ride over to Bunaken and see dolphins and pilot-whales, do some reading etc etc.
If you want to be away from it all, then go over to Bunaken.
Who to dive/stay with?
Manado-side we have dived with lumbalumba for 9 years and their new dive lodge is superb - the web-site is absolutely genuine, although in reality it may actually be rather more beautiful! The cottages are well-appointed with fridge, water-cooler, hot water showers. Personalised service - and some of their guides have been with them for years - still enthousiastic and immensely knowledgeable. Will pick you up at the airport etc etc. Welcoming, good food.
www.lumbalumbadiving.com
On Bunaken there are Froggies - search out Shiri's dive report from last summer and a number of other recommendations on this site. We've been across to Froggies and enjoyed a day there with Christiane and her staff. Welcoming, personalised and good food. Also there have been other recommendations on this site - I think I have Celebes divers recommended. They have web-sites.
If you want cattle-boat diving, please do not try any of the above!