If you're into canals, there is nothing wrong with that section of the Erie - in fact its fascinating. I expected that stretch to be all industrial and commercial, and instead its beautiful and scenic - much of the area between Locks 6 and 7 comprises a wildlife refuge...
I would put my 22' into that section for a few days for sure - hopefully when the weather settles down so the water isnt that fast moving, chocolate brown crap you referred to. Usually its more scenic and tranquil than that!!!
As for other alternatives, sure Lake George would be terrific - we did that last year - but again its a different type of boating and can ironically be rather crowded on summer weekends depending on where you go. Champlain is awesome too - big, open, and best of all, UN-crowded...
So its all a matter of taste...
PS - the dredging on the Hudson is not upstream from the Mohawk, so the PCB thing shouldnt be a factor (if it is anyway)... Unless I am mistaken and there is dredging on the Mohawk too, but I hadnt heard of that...