Can you make the drone home in on blinking LEDs? Make each station an active participant in the process.
I'd do it with Arduinos simulating an IR remote control so that they are sending out a relatively complex signal which can be identified which one it is. Like just holding down the number buttons on a regular remote. Then have the drone rotate until the desired signal is received and move forwards. Descend when the signal is detected on a downward-facing sensor.