RFID enable microcontrllers (ISO14443/NFC) are available from several manufacturers (e.g. Infineon, TI, ST, Nexperia), also smaller EEPROM with RFID interface. The processors have a strong focus on security features which also involves a lack of publically available documentation. A NDA is usually required to receive meaningful documents.
13.56 MHz couplers need a certain size, even if you don't rely on field strength and operation distance presumed in the standards. How big can the interface of your "pen" be?