I am not doing lunges currently due to Iliopsoas bursitis & I often do 1-legged straight leg deadlifts instead. I understand I am getting more hamstring here, although lunges just hurt too much for a week after. I am waiting and stalking craigslist currently for a trap/hex bar to do more controlled/safer deadlifts.
For a squat alternative, you can try those heavy band push backs on all fours (put cushioning under your knees). That isn't going to work in the flow of any boot camp workout etc., but it works for isolation work.