1. Click Settings on the Navigation bar and select Stores & Registers from the drop-down

2. Click on View button viewbutton.jpg  of the Store

3. Store view page shows all the details of the store. Click on the Payment Options tab. This tab shows all the Payment types assigned to the store. Check or Uncheck the checkbox of payment types to enable or disable a Payment type for the store

    Click Save to save the changes made

Refer the following article to know 
How to add a New Payment Type?