I've recently begun finishing my basement. In the mechanical room, I have a series of junction boxes about 2' away from my manablock system and will likely have a sewage ejector pump running overhead in the future...

I'm not a fan of junction boxes and, of course, never hide them; but I was left little choice on this project. The electrician left me a couple of stubs of wire for the circuits in the basement with a couple others run very poorly and without enough slack to run them straight to the fixture.

I may be able to move the junction boxes and re-run a couple of circuits to get more space, but ~4' is all I'll be able to manage. I have a bit of an uneasy feeling about the location, but am I violating any code?

There is no problem, safety issue or code issue with your set up. In fact, as long as they are not touching they can be as close as you can get.

I am personally not sure what this common phobia is with boxes and water lines.

I am NOT suggesting this (obviously), but you could spray those boxes down with a hose and nothing will happen. Other than maybe a GFI tripping.

From what I can see, your electrician did a pretty neat job. (IMO) And the labeling is a bonus.

I was actually the electrician on this job... I was referencing the original electrician... not a criticism though... I didn't pay for a finished basement.