Can we send data from different url's into different index in elastic search using one single logstash config file

Yes you can do it using if conditions in the output section:

input {
    http_poller {
        ...
        add_tag => "source1"
    }
    http_poller {
        ...
        add_tag => "source2"
    }
}
filter {
    ...
}
output {
    if "source1" in [tags] {
         elasticsearch {
             ...
             index => "index1"
         }
    }
    else if "source2" in [tags] {
         elasticsearch {
             ...
             index => "index2"
         }
    }
}