We prefer EPCOT, mostly because you can actually see all of the show from the boat. MK, you can see the fireworks, but miss the projections, which now make up a big part of the show.
There was something *really* magical about the MK fireworks cruise. When we did it, we first cruised around the waterways and watched the Electric Water Pageant from the Poly bungalows before motoring over to the MK entrance to watch Happily Ever After. I would gladly do it again, even if I don't have a great view of the projections.
We've done both and I'd give the edge to the MK cruise. You get a nice cruise around Seven Seas Lagoon and Bay Lake before the fireworks. The viewing location is also perfect. When we did this one the timing worked out so that we saw the Electric Water Pageant before getting back into the GF dock.