Lembeh absolutely. If rare and macro critters are your focus, Lembeh is the bomb. As soon as you get to your resort (or boat) your dive guide will ask you for your wish list. You will most likely see everything on your list plus a bunch of stuff you didn't even know to ask for by the end of your stay. The only thing we didn't see was a blue-ring octopus and that's only because on our last day we had a choice of trying to find it vs. spending some more quality time with the flamboyant cuttlefish and we opted for the cuttlefish instead.
Don't get me wrong, we loved Komodo and still consider it the best all around diving we've ever done, but you can't beat Lembeh for critters.
Also, unless you just love being on boats (and the cramped quarters that go with them), I'd choose a land-based resort instead. The absolute best Lembeh diving is so accessible to land that it just doesn't make sense to me to stay on a boat there. Plus, I'm pretty sure that even the best resorts are cheaper than a liveaboard. All of the best critter sites are clustered in the straits within 10-30 minutes of the resorts. You go out, do a dive, come back, relax, change tanks, go out again, repeat 3-4 times/day. Komodo, on the other, you are much better off on a liveaboard since the sites are so far away from any inhabited islands.
