Funnily enough I co-authored a paper on this last summer...

What we did is took the 1000 values (in our case though we used many millions) and ordered them, smallest to largest. Then you just take the value which corresponds to the percentage point you want.

So for your 1000 values, if you want the upper 5% point, take the 950th values in your ordered set (have to check if we used 950, 951 or a combo of both).