In terms of PH, both are similar although Lemon juice is slightly more acidic in nature. For killing germs in a natural way, using lemons is a better way mainly because it not only kills the germs but also the smell of lemon is more pleasant. Vinegar can be used to clean practically anything largely due to it’s acidity and also the fact that it comes cheap. This is what
the plumber in Toronto advised me regarding Eco-friendly cleaning agents. Since the requirement here is on a large scale, I would suggest it would be better to use lemon juice for the ease of transportation as well as the fact that having a good odor around is always pleasant especially while sailing.
I disagree with you Max...for one thing, we're not talking about CLEANING anything, the ONLY reason to use vinegar in a sanitation system is to PREVENT sea water mineral--and hard water minerals in some fresh waters--buildup in the hoses. For another thing, lemon juice is sticky...distilled white vinegar. DSV is available by the quart in both hardware and grocery (cleaning section) stores, and I've even seen it in gallons....I've never seen lemon juice in anything bigger than a pint.
An undiluted cupful once a week, or as often as you use the boat, is all you need...flushed ALL the way through the system, followed by a clean fresh water rinse (add the fresh water with cup!) after about 45 minutes. It does need to be used regularly to prevent mineral buildup..."every now and then" won't do it.
Do NOT leave it sitting in the bowl! When soft rubber, i.e. your joker valve, is left to soak in vinegar for an extended period, it swells and distorts. Since you're gonna rinse it out of the system after it's had time to do its job each time, it doesn't matter how nice it smells...only whether it works.
Vinegar CAN eventually dissolve a buildup, but it takes so many multiple applications and takes so long to accomplish it that it's not worth the effort. Muriatic acid is about the only way to clean out a buildup, and it's a pain to use. So as is true of most things, prevention is a LOT easier than cure!