That's a tough one. I think my first reaction is you won't be disappointed by either so don't worry.
I am not familiar with Tasik Ria butI have dives a lot in Bunaken, Lembeh and just a little in Malapascua. Ok a lot.
The three locations mentioned are quite different. For me Bunaken is nice but gets repetitive very quickly. The walls are healthy,there are turtles and a nice variety of reef fish. However each wall dive turns into the next, and the next and the next.
Are you planning on Lembeh or Manado only? For me Lembeh is much,much better with some of the world's best macro and critter diving in a small location. I could happily spend weeks there. For the two Indonesian locations I can say for sure that the diving is good but it is very limiting topside. There is not much happening in Manado, even less in Bunaken and 100% nothing in Lembeh. You can expect to basically stay in your resort for the entire stay. But with 4 dives a day that's not so bad over a week.
Finally Malapascua - as you know its the only place to see Threshers but it also has very strong macro. What I like most about Malapascua is its one location but has a real variety of dive styles. It has classic wall diving (Monad Shoal), it has Pelagic encounters (Mantas, Threshers, Mobula at Monad, Hammerheads at Kimud), it has muck diving (Evolution House Reef - seahorses, Crinoid Squat Lobsters, Devilfish, Stargazers etc), it has some incredible soft corals (Bogtong bato, Lapus etc), WWII and more contemporary wrecks (Tapilon, Dona MArylin, Mogami Maru for tech divers) and it has Gato and Kalangamman Island (for cave / tunnel dives and the latter for tropical mind blowing above and below).
Equally for me the Philippines is so relaxed top side with lots of lazy bars selling cheap beers and of course Malapascua has the beach which is great for relaxing and makes it easy to walk up and down from place to place.
As I said, either way you'll be happy. PM me if you need more info. Enjoy!