Amsterdam check in vs flight arrival
 

We arrive in AMS at 9am but wont be able to check in until 2:30. It is an apartment which will be occupied the night before our arrival so they will be cleaning, hence no early check-in available.
Where can we go to rest for a few hours? We will be able to leave our bags at the apartment but I wonder if we should linger at the airport or central station instead.

The apartment is in the Jordaan.

If you can leave your luggage at the apt., then just do an easy day around Amsterdam, take a canaal cruise or hang out in a cafe and watch the world go by. No way I'd hang at the airport or train station! Spend some time in Vondelpark, enjoying the sun and open areas.

By the time you are through Schiphol and into Amsterdam it will be about 10.30. Dump your luggage, go find a cup of coffee, and get a feel for the city. Take a boat trip and relax - you probably won't feel like doing much more than that anyway.
Hopefully there will be some sun for you to enjoy!

Sound advise. Thank you.

Having just returned from Amsterdam, that is exactly what I would do :)