Well, it depends on your needs. For sure Lembeh has larger, roomier boats, with more space to move around in (plus store gear). However they are slower than KBR's fast "speedboats", which may make a difference in terms of getting to the sites quickly, but more than 4 on the KBR boats (and with camera gear) it does get very "tight".
Guide-wise they both have stellar line-ups : LR has Paulus and Samuel who are both legendary for their critter-finding abilities, while I also like Desmond from KBR who is very friendly and accomodating.
Food wise, LR has the better cuisine, better bar, and FAR superior desserts (if you have a sweet tooth?). I also like the service at LR more, it feels much more "personal".
Lastly, be advised that KBR recently had some major management shake-ups and so it may take time for things to settle-in over there. Danny and Ray have been at LR for years and they have a great system in place, and their house reef is diveable in the evenings (which KBR's is not), and the mating mandarinfish are just a short surface swim away every day at 5PM.
Again, I don't know what matters to you most. You can have a nice time at either!
Enjoy!
HB