It's impossible for me to rank the civs because some are good for conquest, some are good for diplomacy, etc. So I'll just briefly talk about a few of them instead:
Askia - Songhai
War Canoe's extra sight and extra strength is a lot less situational than you would think. But it's still just sauce on the side and you're not going to conquer the high seas with a horsey (Mandekalu Cavalry) so they wouldn't be my choice of civ
Dido - Carthage
I'm on the bandwagon that says free harbors makes them one of the best civs. I've seen around these forums people saying that in BNW the benefits are lessened. To those people, I would rethink those thoughts:
http://www.civilopedia.info/civilopedia/BUILDING_HARBOR.aspx I have a BNW game started with them, but I wanted to finish my Indonesia 'learning BNW mechanics' playthrough first
Elizabeth - England
I would have to agree with everyone that England is the best all-around on a water map. But only if you are aggressive. If you want to turtle there are better civs here. Particularly now that the culture and diplomacy game is so deep
Enrico Dandolo - Venice
No idea what to expect. But looking forward to trying out. With my Indonesia playthrough, sea trade routes were very, very lucrative for me (when I wasn't getting my ships plundered all the time...) I was raking in so much cash. Venice + double routes sounds amazing
Gajah Mada - Indonesia
Playing with them right now on small continents. Built 3 cities all on the same continent and spent the entire first part of the game building up my economy and infrastructure. As soon as I could travel across the ocean, I spammed out three settlers and sent them to the nearest separate landmasses - 1. One with a source of iron (which I used for Frigates), 2. One with a whales resource, 3. One with a marble resource. Used my money to buy 3 workshops in each of the new cities, then sent 3 cargo ships to them. The first 2 with food, the other 1 with production since there was enough wheat and food there for the workers to quickly fix up. Then I switched the 2 food cargo ships to production so I had 3 production ships going for a while. I was spamming out all the necessary buildings in the resource cities at a rapid rate and by the time I reached Archaeology I had 6 powerful cities. 4/6 cities were settled on rivers, so I built Candis in them. I only built two Kris Swordsman as support (Ships and Ranged Units were enough), but as it turned out one with the Recruitment promotion assisted me from getting wiped out by the Zulus. I definitely made a lot of mistakes that I won't mention since it's a lot of random minor learning curve stuff which might cost me the victory, but I've had fun nonetheless. Zulu are so annoying though and relentless. Trading all three of my resources (nutmeg, cloves, pepper) for money. Extra gold helping keep my defensive posture against all the aggressive neighbors. The extra happiness is also nice. Exploration tree has helped me immensely.
Harald Bluetooth - Denmark
I've played them only once...I don't know why, but I'm never drawn to picking them. A naval UU in place of the Norwegian Ski Infantry would be nice even though I don't have anything against the NSI (And I don't have anything against it because I never really play it)
Kamehameha - Polynesia
Polynesia gains big time from BNW, and I'm talking about more than just the awesome ability to meet everyone first. Their Moai gain tourism, but I'm talking about more than that as well. I see that as more of a balance issue to keep the Moai from falling behind the curve. Now I don't know for certain since I haven't played them with the new mechanics, but I believe where the Moai truly gains is being able to build your heavy culture chains where the island is shaped favorably. And using your powerhouse cities to send food and production in the case where you sacrifice those in favor of Moai. Nobody seems to mention that, but that's where I anticipate they will get a lot of help
Maria I - Portugal
Really looking forward to playing. No idea what to expect but I believe Ed Beach when he said through his playthrough that he "never had to worry about money or happiness"
Sejong - Korea
Turtle Ships are really great, but with the added incentive in exploring and mapping out your...map (remember, they are the Caravel replacement), they are one of the last civs I would choose on a watery map
Suleiman - Ottomans
They fare better off on domination throughout a Continents map where you can put both the UA and UUs to use, but I could be wrong - you tell me
Theodora - Byzantium
At least after one playthrough, I love the new Piety tree. There is a whole lot for Theodora to work with when she goes Piety + Exploration on a water map. Especially sending those trade routes exerting her religious pressure
William - The Netherlands
Sea Beggars are perhaps my favorite naval unit in the game. UA is often underestimated in my opinion