Property and violent crime rates started dropping in California in the early 90s[1], along with the rest of the country, before three-strikes was enacted. Crime in California has also declined at rates similar to states without three-strikes policies (e.g. Illinois).
Also, the number of homicides specifically peaked in 1993 at 4,096 and dropped almost every year for the next 25 years. It looks like it bottomed out in 2014 and started climbing again.
It's true that rates in other states dropped also. You mentioned Illinois who did not enact a three strikes law (but its neighbors did, as did the federal government). Note that it didn't see improvement on the same scale as California - and now Chicago's murder rate is so bad that it makes the national news almost every week.
I really don't know that the halving of the murder rate should be credited to tougher sentencing, but it coincides pretty well - so well that when I see claims that they have zero effect I can't help but assume that the findings are agenda-driven.
But tough sentencing laws are falling out of favor and being reversed - or partially reversed. Maybe the homicide rate will stay low and 3-strikes laws will be completely discredited.
[1] http://www.ppic.org/wp-content/uploads/crime-trends-1.png