I've been to Lembeh Strait twice this year - once to KBR (Kungkungan Bay Resort) in March, and then to Lembeh Resort last month. Both are first-rate, well-run operations with excellent dive guides who really know their stuff. (Some of the dive guides at both KBR and Lembeh Resort go back to the days when Larry Smith was pioneering Lembeh muck diving at KBR, so anyone who goes back that far will meet up with old friends.)
Both resort have luxurious, comfortable a/c rooms, though there is a difference between the newer (or newly renovated) cabins and some of the older ones at both places. The boats are appropriate for their use, and the DGs and boat crews know how to handle cameras and housings. Both resorts have well-appointed (but not air conditioned) camera work rooms near the dive deck area.
I'd have to give Lembeh Resort a slight edge when it comes to food, and for the nice view of the volcano. Balancing that is the fact that some of the rooms at Lembeh are located up the cliff, which can be quite a climb.
It's worth noting that the management teams at KBR and Lembeh Resort cooperate in planning dives so that their clients don't end up landing on the same site at the same time. This is still a problem with some of the other operations in the area who don't participate in this system.
This is also an issue with visiting live-aboards. We were forced to divert from our planned dive at Nudi Falls one morning when two big tenders from a visiting Phinisi live-aboard (that I won't name here) raced into the dive area (after we had arrived and were finishing gearing up) and dumped twenty divers into the water. But that was just unprofessional, asshole behavior on the part of the live-aboard operator.
Personally, I can't imagine why anyone would want to do Lembeh from a live-aboard when there are such excellent land-based options available. (On one night dive, I noticed that the fleet liveaboard was anchored in the same bay where we were diving. The bay was dominated by a village featuring a local night club from which very loud (and very bad) Indonesian disco music was blasting across the water from terrible, distorting speakers. I remember thinking to myself that I was very glad I wasn't going to be sleeping on that boat that night....
All in all, both KBR and Lembeh Resort are first-class operations. I don't think you could possibly go wrong either way.