ここから３つ目の駅で降りて下さいって英語でなんて言うの？

Using the phrase "you'll want to" is a polite way to tell them what they should do. "From here" lets them know how many stops they need from where they are right now. I hope that this helps :)

Native speakers will say like this: “Get off the train at the third stop”.
There are lots of other ways to say it, but this one is the most accurate and most commonly used.
Here is an example on how to use this in a conversation:
A: When should I get off? I'm new to this line.
B: You'll want to get off at the third stop.

When explaining to someone where to get off the train from a certain stop then you would add 'from here' or 'from this one' so they would know to count the stops

There are a few ways to give someone directions or to tell them where to exit a train. It is also easy to simplify this by just telling the person the number of stops they have to get off or what station they need to exit.

1) "You will need to get off three stations from here."
- This let's the person know that you are using 'here' as the starting point, and they will simply count three more stations until it is time for them to get off.
2) "You'll want to get off at the third station from here."
- This means the exact same as the first sentence. 'the third station' kind of gives the destination a title and lets the person know exactly where and when to exit the train.