Can i configure two Email Service providers in one AEM instance.?

where the each website is having their own email servers

WHen configuring email on AEM out of the box - you have this configuration screen: 

As you can see - there is only fields for: 

• SMTP server host name - the SMTP server that you want to use.
• SMTP server port - the server port to use, Typically this value is 25. 
• Username - the user name for the SMTP user. 
• Password - the corresponding password.

Therefore - there is no option for a 2nd configuration. All AEM sites that use email and MessageServicGateway will use this 1 configuration. 

Now if you really want to have each site on 1 instance use its own mail server - you can code a custom email service that uses the Java MAIL API. Then you can code the configurations in Java. That way - 1 site can invoke customEmailService1 and site2 can invoke customEmailService2. 

For example - in Java: 

 Properties properties = System.getProperties();
 
        // Setup mail server (Depending upon your
        // Mail server - you may need more props here
        properties.setProperty("mail.smtp.host", aHost);
        properties.setProperty("mail.smtp.user", "<valid SMTP user>");

This 1-1 way does not use ootb AEM email cofiguration