The diving around the northern tip of Sulawesi Island, specifically the Bunaken National Marine Park, is widely considered as one of the top ten diving destinations in the world. While Bunaken's fantastic walls are definitely a sight not to be missed, what really sets the whole area apart is the wide diversity of dive sites available. While Bunaken has those famous walls, a little over an hour away by car is the Lembeh Strait, a macro diver's paradise. To the north, the Gangga and Bangka islands are getting increasingly popular for their gentle slopes of soft corals.
When planning your trip, I strongly suggest that you plan on spending some time in the Lembeh area as well as Bunaken or Bangka. There are a nice range of dive resorts along the Lembeh Strait, all of them within 20 minutes' boat ride to the main dive sites. On the Bunaken side of Sulawesi, you have the option of either staying out on Bunaken or Siladen islands, or you can also stay at one of the many resorts on the coast around Manado. Staying on the mainland is desireable if you're traveling with some non-divers as they will have more diversions to choose from.
If you want help planning your trip - the logistics of getting around Indonesia and getting reliable arrangements made can be a bit daunting - then I can highly recommend Safari Tours, a full service travel agency in Manado that can book a wide range of accommodations, as well as land-side tours around North Sulawesi.
If you're looking for primarily a multi-stop dive holiday — which I highly recommend for this area — then check out Murex Dive Resorts. They have resorts or dive operations in all three areas, and their “Passport to Paradise” allows you to pick how much time you want to spend in each. They'll also take care of all the logistics, so you can get on the dive boat in one place in the morning, get off in the next location after a couple of dives, and all your stuff will be there waiting for you.