The Bay is a must see sight, yes sometimes what the tourists books say you should do sucks but this time I would say this is an attraction that one should put ones prejudice aside and just do what the book says, in other words it was be insane to go to Vietnam and not experience this.
For cruises there are 100 of boats you can chose from and quite frankly it can be both overwhelming and intimidating. Out of randomness and some help from are hotel we picked a 2 day 1 night cruise with Avola Gold Cruises and it was great. 
Our tour guide was great, the itinerary was great, the rooms and boat where way above standard, the only minor criticism i have was the food, and I must really stress minor, for the record I am a food snob and for all the cruises I have been on I have learned to expect that the food is a dumbed down bland westernized versions of the local cuisine. 
Although this again was true it was still way, way above average and lets be frank are any of the other boats going to do it much better. You go to the Bay to experience the nature and this Alova Gold Cruise got right in style and with top notch service and accommodation.