You should choose your liveaboard first, and then let the operator suggest your flights (if needed) to the jump-off point for the cruise. They often want to get everybody they can on the same flight from Bali to facilitate transfers, and it's most often easiest for the operator to arrange for your domestic Indonesia flights anyway, since international credit cards are often not even accepted.
I agree that if you come into Indonesia early (a good idea in case of delays or misdirected luggage issues), you'd be better off staying on Bali than staying at Labuan Bajo.
As for a good boat, well, there are many, and it depends a lot on your trip length and the kind of boat you like, not to mention your budget. All that anybody can really say, in a forum reply, is that they personally had a great time on (whatever) boat. The boat that will best meet your needs, however, might not even be mentioned!
I agree that if you come into Indonesia early (a good idea in case of delays or misdirected luggage issues), you'd be better off staying on Bali than staying at Labuan Bajo.
As for a good boat, well, there are many, and it depends a lot on your trip length and the kind of boat you like, not to mention your budget. All that anybody can really say, in a forum reply, is that they personally had a great time on (whatever) boat. The boat that will best meet your needs, however, might not even be mentioned!