I've been to Yap over 70 times over the years and have watched the development of the two hotels. I've also stayed at both places but it was a few years ago at Yap Pacific. Both are priced similarly and both will take you to the same destinations. The difference is that Manta Ray Bay was and continues to be totally designed for divers, and from the minute you walk in there the "feel" (should have said ambience) of the place begins to take you over.
The rooms are big and comfortable, the showers are big enough to put a bed in, it's a very short walk (1 min) to the dive locker, photo equipment tables, lobby, no horizon pool, and the best damned restaurant/bar in Micronesia..the Mnuw.
The crew handles everything and your gear is set up on the boats, water, tea, and snacks between dives, and when you return it's about 30 ft to the five rinse tanks and drying areas. Oh yeah, they'll take your gear off the boat to the rinse areas also.
The staff is not "plasticized" and when they say hello they really mean it. That's the overall feeling you get there every day.
I could go on and on but then it would become a commercial.
To see what I mean watch this. I did it for a group I took there in 2012. Have fun.