How can I measure thread waiting time?

Try this:

long startTime = System.nanoTime();
methodToTime();
long endTime = System.nanoTime();

long duration = endTime - startTime;

Time it using Sytem.nanoTime(); just before and after the wait.

long start = System.nanoTime();
wait();
long time = System.nanoTime() - start; // nanos

Or:

long start = System.nanoTime();
synchronized (objHere)
{
    long time = System.nanoTime() - start; // nanos
    // ...
}

Note: If a Thread is locked, the scheduler will continue with other Threads. You don't have to do this manually. That is the idea of threads. Maybe you are facing a deadlock? Wikipedia says it nicely:

A deadlock is a situation in which two or more competing actions are each waiting for the other to finish, and thus neither ever does.

Generally the methods which operates on locks accepts timeout as an argument. If you are using wait(), you can specify the amount of time by passing time to wait as argument. Check here for more details: http://docs.oracle.com/javase/7/docs/api/java/lang/Object.html#wait%28long%29.

If you are using Lock, then try tryLock method of it which accepts time it has to wait. Check this tutorial for an idea: http://docs.oracle.com/javase/tutorial/essential/concurrency/newlocks.html