Are you sure they replaced the timing chain? That usually is not a wear item, doesn't really need to be changed, unless you have a lot of miles on the car or if the engine was screwed up to begin with.
As for the knocking noise - could be nearly anything. The 1ZZ-FE engine is not known to be very quiet - to help narrow down the possibilities, it is a higher pitched, clear, metallic tapping or knocking, or a lower pitched, heavy, dull thumping or knocking sound. If the former - could be bad valve clearances, of the timing chain is not tensioned correctly (worn timing guides, sticking tensioner, poor lubrication, VVT-i issue, piston slap, etc.). If it is the later - then could be anything from poor lubrication to rod rod (worn rod bearings, worn crank journals, something bent or cracked, etc.).
What kind of mileage is on the car and what is the maintenance history of it - ie, how often do you change the oil, what oil weight, burns any oil, etc.?