I'd have to say it's a tie... with some variations...between CH-46Ds and CH-47Cs
The most reliable helicopter I crewed and the one I logged the most flight time in was a CH-46D 154831 while I was with HMM-164.
On the other hand the helicopter that I put the most blood, sweat and tears into while getting rid of it's reputation as a "Hangar Queen" was a CH-47C 67-18546 while I was with the 213th Avn Co from 1981 to 1984 . I hid a bunch of incoming parts (ECL control box, LCT link, Fwd Swiveling Actuator, various guages, power steering control box, forward swashplate drive arm link...etc) from our maintenance officer long enough to get them on the aircraft and then convince him it was easier to get the parts he wanted through the supply system rather than arguing with me to get them before I installed them.
It took me six months to get the aircraft flyable and I wound up extending on what was a year long tour to three years because of that aircraft and when I came back to the same unit (87-90), I tried hard to get the same aircraft but had to settle for 74-22278 instead.
Yeah, D model '47s were somewhat less problematical, but on C models you HAD to be mechanically inclined and be able to really troubleshoot systems instead of just changing parts/boxes and hoping the problem would go away.
F Models? Well, if the ones I am around now are any indication, they seem to have too many avionics/electrical problems. It seems as if some people somewhere had a bet as to how much electrical crap they could hang on a Chinook and have it still work while shaking the crap out of said equipment.
(BTW, I work at AFTD at Redstone)