I would think there is a difference in "Visa Service", which this company can provide, and "Visa", which the government gives you. Of course OP will have the details, but the visa service is likely the arrangement of the Visa on Arrival letter, typically about 10 to 20 bucks depending on who you use. OP would likely still have to fill out the forms, bring the picture and paperwork, and get the visa when landing in Hanoi (or SGN or DAD) by paying the cash fee. The free service might also include the expedited service where they have a guy meet you at the airport and help you get the visa.
And, FWIW, visa fees have been reduced. OP doesn't mention what passport they're holding, but the general tourist visa on arrival is now $25 instead of $45. Many European nations now have visa free waiver for up to 15 days stay.
Regarding choosing a tour, there are many "travel agents" and boats who also do the 2 day 1 night cruises that you can join the day of. Most of the boats in my experience are similar and run the same general route. I would also probably just show up if you're looking for the best deal. But if you're less comfortable with that plan it seems, my Vietnamese American friends have been using "tour radar" site lately to book tours here as they like to plan ahead. The lonely planet forum often has good budget travel advice, you might check there. Or just wait until you're in country and book at a local agency near your hotel your first night here, if you're not going straight to Ha Long from the airport. My one caveat is there are some holidays in April/May timeframe, so google it and if you're coming during a holiday then I would book in advance.
I don't know of any boats in particular to recommend though, sorry. 3 star here usually means more like what I consider 1 or 2 star at home in America, so be prepared.
