Tough one.
I tried different ones, I didn't like Blue Marlin at all despite their speed boat, they had very mundane bule guides. I am not especially keen on people overplaying the "everything is so cool" act when they don't deliver, probably my X-generation self surfacing.
My favor would go to Dragon Dive at the time they had a speedboat as well, I think they don't operate it anymore. Their place is also nice to stay.
I usually I don't do liveaboard but IMO it's still the best way to dive Komodo since you can't daytrip to the south, they have plenty of cheap and short liveaboards (4-5 days) that would allow you to cover many more spots than with daytrips, especially in november.