There is a quirk in DB's booking system: whereas you can book special offer tickets and full-fare tickets on the CNL from Amsterdam to Basel SBB, you can't book the sleeper supplement only.

The solution is to book online from Amsterdam to Basel Bad, the last stop in Germany. Then miraculously the "extra charge only" option opens up. No-one will have a problem with you going on to Basel SBB (since presumably your pass will be valid in Switzerland).

If you are worried about availability - book now. You don't have to have bought your pass already, and the cancellation charge up to day before departure is only 10% (so about €10). If you are travelling on the train departing on 6th June from Amsterdam, there is availability (at the time of this post - just checked!).