i would go with the eco boost, with all the RnD work that thay did on it, my gfs dad works at the windsor engine plant next to the dyno room and the 5.0 truck based engine is prity much maxed out, out of the box he was sayin that it only shares some parts with the 5.0 in the stang block heads. The internals are the down fall. The stang engine is based from the ause 5.0. The 3.5 eco boost is the top dog in the dyno room he said the word is thay have had them up to 20psi and 8,000 rpm. and over 600+ hp...
Based on the info I found, the motor is the same with the exception of some changes done mostly for reasons of drivability over max hp, what truck owners would likely want...
Replacing the tried-and-tired 5.4-liter V-8 as the F-150’s volume engine will be the gutsy, all-aluminum, DOHC 5.0-liter V-8 that we’ve fallen in love with in the 2011 Mustang GT. It, too, receives truck-specific tweaks that diminish its overall power in the name of better drivability, but it will produce a still-respectable 360 hp at 5500 rpm and 380 lb-ft of torque at 4250. Major changes separating it from the version in the Mustang are a lower 10.5:1 compression ratio, a revised engine-management system, new intake camshafts with shorter duration, and new cast-iron exhaust manifolds.
I have seen nothing to indicate that the crank, pistons, rods etc are any different. I'm not saying it's not possible, but I haven't seen anything from a reputable source saying otherwise.
The 5.0L motor will be, according to Ford, the most ordered motor in the F150 line-up and IMO, will be every bit as good as Ford enthusiasts want it to be.
I think the Eco Boost is a great motor. And remember, it's been doing duty in the Ford Taurus SHO and the optional motor in the Flex for the last year. It's got lots of real life testing done. It's a $1000 premium over the 5.0L, but I think that's fair considering it does come with some perks...
It makes only 5hp more than the 5.0L, but 40 more ft-lbs/tq - with slightly better fuel economy, and towing capacity increases to 11,300lbs (with the towing package).
This motor's design will ultimately be the future for pick up trucks. All the manufacturers need to meet increasingly strict CAFE standards and going with smaller displacement motors and lighter materials is what's going to help them get there.
Which brings me to another point... A Super Crew F150 is a big vehicle. It's not light. Ford can put whatever motor they like in there, but it still has to motivate over 5000lbs.
As far as the OP's question goes... I personally don't think you'll be disappointed with either motor. If you like the traditional sound of the V8, then go for the 5.0L. If exhaust note isn't so important but more towing ability and a bit better fuel economy is of prime concern, then plop down the extra $1000 and give the new Eco Boost a try.