Hummm, I love Bali and have been 4X's. Definitely the culture & landscape beauty massage, romantic dinners, and shopping beats Manado hands down. Tulemben has nice reef diving and there is a nice drop off for coral. Also Manta Point is a must do! & Mangellan is nice.
I went to Bunakan/Lembeh last year. As far as diving goes. Bunakan is better than the places I've been in Bali in some ways. It's an island and diving is the main attraction. Lots of scuba, beach bar and if you get adventurous jungle walks. The diving is largely wall diving, turtles, sometimes sharks, lots of crabs and lots of colorful coral. It's a great place for beginners & there are some advanced dives there too. The night dives are amazing! Yes I absolutely agree Lembeh is mandatory. But keep in mind alot of the diving at Lembeh is not that beautiful. It's really for fish geeks :blinking:. Muddy bottom with 30-40 ft vis. The cool thing is the critters. Amazing muck diving & the most amazing sea life you've ever seen. It is not a place for beginners though as you must have good control of your buoyancy & lots of the critters are poisonous.
If you have a month of vacation, consider both! Airasia.com flies from Denpasar, through Kuala Lumpur and over to Manado (and if booked early is usually reasonable)!