I just checked out of the Wharf Doubletree yesterday. I enjoyed the property: small, super quiet, nice Diamond recognition and good quality breakfast included.
The ferry ride is easy, even fun, but certainly something to factor in if you need to pop back to the room for some reason throughout the day. Not convenient if you're back and forthing.
I liked the property. Staff was super, everything new and clean.
The DT by Centraal Station would be much easier to access from town and airport/train, of course. Had a lounge upstairs and a Starbucks right in the lobby.
I would have probably stayed at the Centraal property, but they didn't have availability the third day of my trip, so instead of hopping around, I just went with the Wharf DT. Glad I did, but I'm a very light packer and didn't need to haul bags down to the ferry and all that. If you're a large luggage type, go with the in town properties. I imagine the in town ones are nowhere near as quiet as the DT Wharf would be.