As far as I know, you can not pass @Input() to a bootstraped component.

But you can use another way to do that - pass the value as an attribute.

index.html :

<my-app myAttribute="myAttributeValue">
    <div>Loading...</div>
</my-app>

app.component.ts :

@Component({
    selector: 'my-app',
    templateUrl: 'app.component.html',
    styleUrls: ['app.component.css']
})
export class AppComponent {
    constructor(private elementRef:ElementRef) {
        let myAttribute = this.elementRef.nativeElement.getAttribute('myAttribute');
    }
}

As @Grégory Gossart said you can not pass @Input data as normal for bootstraped components.

It is because an @Input is expected to come from an angular component. So, If your root app is loaded/bootstraped directly in the HTML it has not reference of what Is gonna provide that @Input, I thought.

As good practice commented on many Angular docs, and probably because it specific behaviours, you should only bootstrap one root App. I think your option here is add a root app which you bootstrap and it imports your others(3) and use those as template in it. Then pass the @Input as normal. Really nothing special.

I think another option could be pass the data from an @Injectable to your root apps if you decide you need to bootstrap all them and need external data. But I feel it is more refered to specific purposes.

Edit: I took a time to find this blog I have read past day and reason why I said about @Injectable. So merits to the author, but interesting stuff. Providing external data when bootstrapping Angular 2