So, late as hell to the thread...
When I went looking, and I was looking for used (1-2 years old), I couldn't find an Ecodiesel, but in retrospect I'm kinda glad I didn't.
1) Now if I were hauling stuff heavier than the ~5,000 lb limit my little V6 gives me (w/ a 3.21 axle), then the Ecodiesel would be the way to go, since max towing would shoot up to 8,000+ lbs. But, I don't, so there was no real justification in my spending the dosh to do that.
Most boats are clearly lighter than 5k (and it'd be hard to find a 17' boat that would even come close to 3,000 lbs, even fully-laden), so that's probably not going to be sufficient justification.
2) Ecodiesel gets ~28mpg, Pentastar gets around 24mpg. Four miles per gallon ain't gonna really be enough to justify the $4.5k price difference, higher maintenance costs, all that stupid DEF fluid, etc.
...however, uncertainty plus differential in gasoline vs. diesel prices may someday cover the difference, especially back in 2012 when gasoline shot up to around $4.50/gal out here in Oregon, but diesel still hovered down around $2.50/gal or so. It was a double-whammy that would have made diesel a way smarter buy, especially if the prices had stayed where they were (or gas got even worse). But... we're wandering off into gambling/prophesy territory here.
3) Finding a diesel pump in some areas is damned hard to do (at least out here), especially when most local consumer (not commercial) gas stations might have one diesel pump (if it ain't out-of-order), and it'll likely be a crap-shoot as to whether it'll be diesel type #1 or #2 going into your tank. You can get around that by hitting the truck stops and getting your fuel there... if there's one close by to home and/or work.
Overall, I decided on the V6 gasser, partly by Hobson's Choice. I'm glad I did. However, I'm not you... so you may want to take a good, hard look at what you want to do, where you think things overall are going, and whether or not one option over the other makes the most sense.