I don't need to change the color of LED. Just on and off of the led using wifi/bluetooth is sufficient.
Question: how many leds would ever be on at once?
If the answer is only one, such as a circuit which lights up a led on a large map to indicate a location, there may be a way to do this with minimal circuit using a technique called charlieplexing.
If the answer is that all 1000 could be on at once, then another way would be to use 16 max7219 chips. Each chip could drive 64 leds. Whether this would work out cheaper than Mike's suggestion, you would have to shop around and "do the math(s)"