Part of Manuel Antonio is in a national park, so the beach there is totally unspoiled (and probbaly one of the best beaches around). However, once you step outside outside the park you have a host of small restaurants, B&B and hotels. While not exactly a resort feel like say Conchal, it's not a exactly desolate.
I would probably go to MA first, then Monteverde; if it's not to your liking you can always cut the stay there short and explore other places (say Arenal or maybe even head to Guanacaste). 3 nights in San Jose might be 1 night too much.