Pedals aren't the whole solution here- they help, but knee alignment problems usually take more than that. I have a giant box of pedals that I went through before my knees gave out completely. They just staved the problem off.This is not an uncommon situation with cyclists, ther's this beleif that a new gizmo will fix it when that's not usually the case. Shops do very well on this. Two cheaper quick fixes are orthotics, which any Gita dealer can get you for about thirty bucks. The good ones are called Peterson Powerbeds. Or you may need custom ones, go to an orthoticist, not a physical therapist for them. The obvious joint problem is often caused by a problem in the next joint. Foot problems cause a lot of knee trouble.
Big Meat Cleat adjusters will fix a lot! I already mentioned these. What the average bike shop guy doesn't know is that all the high level riders use both of these. Every Tour rider has orthotics, and if not cleat wedges then the shoes and cleats have been taken to a machine shop and customized. The basic fitting you get at the average shop is usually ok, but the kind of biomechanical problems that chew up a knee or haul on the SI joint are beyond the scope of most of these guys knowledge. Unless your shop is fitting nationally competitive racers, then they know more, but unless you make noise you aren't going to get that attention. The guy who really knows what he's doing will put you on the trainer and watch you spin.
Crosstraining helps too. If all you do is ride, and your tecnique is less than stellar, muscle imbalance will pull you out of whack.