i'm not a huge fan of the highland park bridge because of the speed and density of traffic. it's not that i fear for my safety, really, it's just that it can be nerve-wracking. i'm riding a bike because it's the more enjoyable mode, and i don't want that enjoyment lessened because jagoffs have to cross the river at 60 mph.
on 62nd street, the traffic may reach the same speeds, but i only ever get passed by like one or two cars either direction (granted, i'm usually not traveling through there at rush hour).
the problem with 62nd is, as almklm said, the ride up through the zoo is pretty nice, and you'd have to backtrack to get there.
that said, i guess my preferred route to waterworks would be: ellsworth -> negley -> stanton -> chislett -> greenwood -> morningside -> baker -> butler -> 62nd street bridge -> main -> freeport.
on the return, i'd probably go 62nd -> butler -> main -> liberty, or maybe do a wiggle on hot or tired days.