What can I do that gives me close to the same benefit ? My knees tend to hurt for a few days after this accessory !
The first thing I would do is make sure you are doing the PISTON squat, and not the Pistol squat. Two very different movements!
The piston squat is great for building the quads, while the pistol squat is a single leg movement requiring a lot of mobility and places a large amount of sheer force on the knee.
Here is a link to each movement
If you are in fact doing a PISTON squat, and are having knee pain, I would make sure that you are sitting back into the squat as you normally would, in order to tension the hamstrings. If you continue to have some knee pain, I think taking some time away from the movement, performing some corrective exercise like TKE and glute med activation to relieve the strain on the patellar tendon. It may not be the most optimal movement for you.
If you have access to a leg press machine you can replicate a piston squat while playing around with foot position. I also like to use Bulgarian split squats for quad work. Backward sled drags are another favorite.