To say thank you for graduation money, write a handwritten note expressing gratitude for the person's generosity. Proper etiquette maintains that it should not be framed as a gift of money.
Etiquette experts recommend drafting a personal note for those people who provided gifts for a graduation. Even if there is an opportunity to express your thanks via phone, it's still recommended that the recipient drafts a formal note.
The note should express gratitude, but should also address how the gift will be used. For recent graduates, it could be used to help purchase books for class or to save up for a study-abroad program.