As you are using Spring Boot web, Jackson dependency is implicit and we do not have to define explicitly. You can check for Jackson dependency in your pom.xml in the dependency hierarchy tab if using eclipse.

And as you have annotated with @RestController there is no need to do explicit json conversion. Just return a POJO and jackson serializer will take care of converting to json. It is equivalent to using @ResponseBody when used with @Controller. Rather than placing @ResponseBody on every controller method we place @RestController instead of vanilla @Controller and @ResponseBody by default is applied on all resources in that controller.
Refer this link: https://docs.spring.io/spring/docs/current/spring-framework-reference/html/mvc.html#mvc-ann-responsebody

The problem you are facing is because the returned object(JSONObject) does not have getter for certain properties. And your intention is not to serialize this JSONObject but instead to serialize a POJO. So just return the POJO.
Refer this link: https://stackoverflow.com/a/35822500/5039001

If you want to return a json serialized string then just return the string. Spring will use StringHttpMessageConverter instead of JSON converter in this case.

You can simply return an object with those attributes. For example declare a new class that represents your desired response:

public class UserResponse {
    private Boolean status;
    private String message;
    private List data;

    public UserResponse(){
    }

    // setters & getters
}

And then change your controller:

@GetMapping("/users")
public UserResponse getAllUsers() {
    List<User> user = repository.findAll(); // get all users from db

    UserResponse userResponse = new UserResponse();

    userResponse.setStatus(true);
    userResponse.setMessage("Data is found");
    userResponse.setData(user);

    return userResponse;
}

For an in depth explanation of what was wrong with your approach you can check this answer

If you are using the spring-boot-starter-web, your project is already set to return JSON. Instead of String as the return value from checkEmailUnique, use an object type that you create.

Here is an example:

public class EmailStatusCheckJson
{
    private Boolean emailIsAvailable;

    public Boolean getEmailIsAvailable()
    {
        return emailIsAvailable;
    }

    public void setEmailIsAvailable(
        final Boolean newValue)
    {
        emailIsAvailable = newValue
    }
}


@RequestMapping(value="/checkEmailUnique",method=RequestMethod.POST)
public EmailStatusCheckJson checkEmailUnique(@RequestBody final String username)
{
    final EmailStatusCheckJson returnValue = new EmailStatusCheckJson();

    if (...) // email is available.
    {
        returnValue.setEmailIsAvailable(true);
    }
    else
    {
        returnValue.setEmailIsAvailable(false);
    }

    return returnValue;        
}

Edited added more example.