Hmmm...these are both older systems, its hard to really be sure. However:
For starters you'll have to describe the systems better: do they come with autoinjectors, or will you syringe inject each sample? That can get tedious as you try to validate. What model of Waters autoinjector will you get?
The HP1050 is more of a modular system. Its meant to go together with other 1050 components, stacked together, with short path-lengths between components. The Waters 600 system is a big old box, just because you can stack components, doesn't mean they're as "close"as the 1060 system.
Ease of finding parts is a little tricky. Before you buy either, call both Waters and HP and find out what sort of service plan they offer. They want to help,once you make some money you may buy their next gen system. But they may be limited in the help they can give you.
I'm somewhat biased towards Waters software over HP. Lots of people share this bias. There's nothing wrong with HP's software, except some of its functions are a little too ... "engineering", when they could be more "push button" as they are on Waters. Again, I don't know what software you're going to get for these systems either.